ゲストやルート、別ユーザーでログインした時に問題ないのでしたら、ホームを再生成してみるとどうでしょうか。
各種設定もデフォルトに戻ります。

「ユーザーとグループ」の高度な設定やコマンドからも出来ますが、メールやブラウザの名前の付いたファイルやフォルダは退避させて、後に上書きして元に戻して下さい。

荒っぽいやり方としては、ホームフォルダの中身を隠しファイルを含む全てを移動させます。
空っぽになったホームフォルダには必要なファイルがデフォルトの設定で再生成されますので、その後に個人の設定ファイルをホームに戻す。です。

launchpadの方で同じような内容の報告が出てますね。（未解決）
https://bugs.launchpad.net/ubuntu/+sour … bug/516331

pc944さんは別のトピックで10.04での質問をだしているので、この問題が9.10なのか10.04なのかが気になります。
10.04のほうでしたら、もうしばらく様子を見てみては？
9.10だったらlaunchpadの方にご自身も影響を受けている人として追加されるとよろしいかと思います。

Xorg.0.log

X.Org X Server 1.7.6
Release Date: 2010-03-17
X Protocol Version 11, Revision 0
Build Operating System: Linux 2.6.24-23-server i686 Ubuntu
Current Operating System: Linux ****-my-laptop 2.6.32-19-generic #28-Ubuntu SMP Wed Mar 31 17:46:20 UTC 2010 i686
Kernel command line: BOOT_IMAGE=/vmlinuz-2.6.32-19-generic root=UUID=84503018-e39b-49c5-bebc-38a3fd6f16de ro vga=769 quiet splash nomodeset
Build Date: 08 April 2010  11:54:08PM
xorg-server 2:1.7.6-2ubuntu2 (Bryce Harrington <[email protected]>)
Current version of pixman: 0.16.4
    Before reporting problems, check http://wiki.x.org
    to make sure that you have the latest version.
Markers: (--) probed, (**) from config file, (==) default setting,
    (++) from command line, (!!) notice, (II) informational,
    (WW) warning, (EE) error, (NI) not implemented, (??) unknown.
(==) Log file: "/var/log/Xorg.0.log", Time: Mon Apr 12 07:09:01 2010
(==) Using config directory: "/usr/lib/X11/xorg.conf.d"
(==) No Layout section.  Using the first Screen section.
(==) No screen section available. Using defaults.
(**) |-->Screen "Default Screen Section" (0)
(**) |   |-->Monitor "<default monitor>"
(==) No monitor specified for screen "Default Screen Section".
    Using a default monitor configuration.
(==) Automatically adding devices
(==) Automatically enabling devices
(WW) The directory "/usr/share/fonts/X11/cyrillic" does not exist.
    Entry deleted from font path.
(==) FontPath set to:
    /usr/share/fonts/X11/misc,
    /usr/share/fonts/X11/100dpi/:unscaled,
    /usr/share/fonts/X11/75dpi/:unscaled,
    /usr/share/fonts/X11/Type1,
    /usr/share/fonts/X11/100dpi,
    /usr/share/fonts/X11/75dpi,
    /var/lib/defoma/x-ttcidfont-conf.d/dirs/TrueType,
    built-ins
(==) ModulePath set to "/usr/lib/xorg/extra-modules,/usr/lib/xorg/modules"
(II) The server relies on udev to provide the list of input devices.
    If no devices become available, reconfigure udev or disable AutoAddDevices.
(II) Loader magic: 0x81f0e80
(II) Module ABI versions:
    X.Org ANSI C Emulation: 0.4
    X.Org Video Driver: 6.0
    X.Org XInput driver : 7.0
    X.Org Server Extension : 2.0
(++) using VT number 7

(--) PCI:*(0:1:0:0) 1039:6325:1033:821a Silicon Integrated Systems [SiS] 65x/M650/740 PCI/AGP VGA Display Adapter rev 0, Mem @ 0xf0000000/134217728, 0xec300000/131072, I/O @ 0x0000a000/128
(II) Open ACPI successful (/var/run/acpid.socket)
(II) LoadModule: "extmod"
(II) Loading /usr/lib/xorg/modules/extensions/libextmod.so
(II) Module extmod: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.0.0
    Module class: X.Org Server Extension
    ABI class: X.Org Server Extension, version 2.0
(II) Loading extension MIT-SCREEN-SAVER
(II) Loading extension XFree86-VidModeExtension
(II) Loading extension XFree86-DGA
(II) Loading extension DPMS
(II) Loading extension XVideo
(II) Loading extension XVideo-MotionCompensation
(II) Loading extension X-Resource
(II) LoadModule: "dbe"
(II) Loading /usr/lib/xorg/modules/extensions/libdbe.so
(II) Module dbe: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.0.0
    Module class: X.Org Server Extension
    ABI class: X.Org Server Extension, version 2.0
(II) Loading extension DOUBLE-BUFFER
(II) LoadModule: "glx"
(II) Loading /usr/lib/xorg/modules/extensions/libglx.so
(II) Module glx: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.0.0
    ABI class: X.Org Server Extension, version 2.0
(==) AIGLX enabled
(II) Loading extension GLX
(II) LoadModule: "record"
(II) Loading /usr/lib/xorg/modules/extensions/librecord.so
(II) Module record: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.13.0
    Module class: X.Org Server Extension
    ABI class: X.Org Server Extension, version 2.0
(II) Loading extension RECORD
(II) LoadModule: "dri"
(II) Loading /usr/lib/xorg/modules/extensions/libdri.so
(II) Module dri: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.0.0
    ABI class: X.Org Server Extension, version 2.0
(II) Loading extension XFree86-DRI
(II) LoadModule: "dri2"
(II) Loading /usr/lib/xorg/modules/extensions/libdri2.so
(II) Module dri2: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.1.0
    ABI class: X.Org Server Extension, version 2.0
(II) Loading extension DRI2
(==) Matched sis as autoconfigured driver 0
(==) Matched vesa as autoconfigured driver 1
(==) Matched fbdev as autoconfigured driver 2
(==) Assigned the driver to the xf86ConfigLayout
(II) LoadModule: "sis"
(II) Loading /usr/lib/xorg/modules/drivers/sis_drv.so
(II) Module sis: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 0.10.2
    Module class: X.Org Video Driver
    ABI class: X.Org Video Driver, version 6.0
(II) LoadModule: "vesa"
(II) Loading /usr/lib/xorg/modules/drivers/vesa_drv.so
(II) Module vesa: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 2.3.0
    Module class: X.Org Video Driver
    ABI class: X.Org Video Driver, version 6.0
(II) LoadModule: "fbdev"
(II) Loading /usr/lib/xorg/modules/drivers/fbdev_drv.so
(II) Module fbdev: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 0.4.1
    ABI class: X.Org Video Driver, version 6.0
(II) SIS: driver for SiS chipsets: SIS5597/5598, SIS530/620,
    SIS6326/AGP/DVD, SIS300/305, SIS630/730, SIS540, SIS315, SIS315H,
    SIS315PRO/E, SIS550, SIS650/M650/651/740, SIS330(Xabre),
    SIS660/[M]661[F|M]X/[M]670/[M]741[GX]/[M]760[GX]/[M]761[GX]/[M]770[GX],
    SIS340
(II) SIS: driver for XGI chipsets: Volari Z7 (XG20),
    Volari V3XT/V5/V8/Duo (XG40)
(II) VESA: driver for VESA chipsets: vesa
(II) FBDEV: driver for framebuffer: fbdev
(II) Primary Device is: PCI 01@00:00:0
(WW) Falling back to old probe method for sis
(--) Assigning device section with no busID to primary device
(--) Chipset SIS650/M650/651/740 found
(WW) Falling back to old probe method for vesa
(WW) Falling back to old probe method for fbdev
(II) Loading sub module "fbdevhw"
(II) LoadModule: "fbdevhw"
(II) Loading /usr/lib/xorg/modules/linux/libfbdevhw.so
(II) Module fbdevhw: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 0.0.2
    ABI class: X.Org Video Driver, version 6.0
(II) SIS(0): SiS driver (2005/09/20-1, compiled for X.org 1.7.6.0)
(II) SIS(0): Copyright (C) 2001-2005 Thomas Winischhofer <[email protected]> and others
(II) SIS(0): *** See http://www.winischhofer.at/linuxsisvga.shtml
(II) SIS(0): *** for documentation and updates.
(--) SIS(0): sisfb not found
(--) SIS(0): Relocated I/O registers at 0xA000
(II) Loading sub module "ramdac"
(II) LoadModule: "ramdac"
(II) Module "ramdac" already built-in
(II) SIS(0): Creating default Display subsection in Screen section
    "Default Screen Section" for depth/fbbpp 24/32
(==) SIS(0): Depth 24, (--) framebuffer bpp 32
(==) SIS(0): RGB weight 888
(==) SIS(0): Default visual is TrueColor
(WW) SIS(0): Could not find/read video BIOS
(==) SIS(0): Using XAA acceleration architecture
(==) SIS(0): Using HW cursor
(==) SIS(0): Color HW cursor is enabled
(II) SIS(0): Using VRAM command queue, size 512k
(==) SIS(0): Hotkey display switching is enabled
(II) SIS(0): WARNING: Using the Hotkey might freeze your machine, regardless
(II) SIS(0):          whether enabled or disabled. This is no driver bug.
(==) SIS(0): SiSCtrl utility interface is disabled
(II) SIS(0): For information on SiSCtrl, see
        http://www.winischhofer.at/linuxsispart1.shtml#sisctrl
(==) SIS(0): DRI disabled
(II) SIS(0): Checking OS for SSE support is not supported in this version of X.org
(II) SIS(0): If your OS supports SSE, set the option "UseSSE" to "on".
(--) SIS(0): DIMM0 is DDR SDRAM
(--) SIS(0): DIMM1 is not installed
(--) SIS(0): DIMM2 is not installed
(--) SIS(0): DIMM3 is not installed
(--) SIS(0): DRAM type: DDR SDRAM
(--) SIS(0): Memory clock: 200.452 MHz
(--) SIS(0): DRAM bus width: 64 bit
(--) SIS(0): Linear framebuffer at 0xF0000000
(--) SIS(0): MMIO registers at 0xEC300000 (size 64K)
(--) SIS(0): VideoRAM: 32768 KB
(II) SIS(0): Using 32192K of framebuffer memory at offset 0K
(--) SIS(0): Hardware supports one video overlay
(--) SIS(0): Detected SiS302LV video bridge (Charter/UMC-1, ID 1; Rev 0xe1)
(--) SIS(0): No CRT1/VGA detected
(--) SIS(0): Detected LCD/plasma panel (1024x768, 1, exp., RGB24 [02f200])
(==) SIS(0): Using gamma correction (1.0, 1.0, 1.0)
(II) SIS(0): CRT1 gamma correction is enabled
(II) SIS(0): Separate Xv gamma correction for CRT1 is disabled
(II) SIS(0): CRT2 gamma correction is enabled
(--) SIS(0): Using Xv overlay by default on CRT2
(--) SIS(0): Memory bandwidth at 32 bpp is 400.904 MHz
(--) SIS(0): Detected LCD PanelDelayCompensation 0x02 (for LCD=CRT2)
(--) SIS(0): Detected LCD PanelDelayCompensation1 0x00 (for LCD=CRT1)
(--) SIS(0): 302LV/302ELV: Using EMI 0x00001008 (LCD)
(II) Loading sub module "ddc"
(II) LoadModule: "ddc"
(II) Module "ddc" already built-in
(--) SIS(0): CRT2 DDC probing failed
(==) SIS(0): Min pixel clock is 10 MHz
(--) SIS(0): Max pixel clock is 278 MHz
(II) SIS(0): Replaced entire mode list with built-in modes
(II) SIS(0): Correcting missing CRT2 monitor HSync range
(II) SIS(0): Correcting missing CRT2 monitor VRefresh range
(II) SIS(0): "Unknown reason" in the following list means that the mode
(II) SIS(0): is not supported on the chipset/bridge/current output device.
(II) SIS(0): <default monitor>: Using hsync range of 30.00-80.00 kHz
(II) SIS(0): <default monitor>: Using vrefresh range of 59.00-61.00 Hz
(II) SIS(0): <default monitor>: Using vrefresh value of 71.00 Hz
(WW) SIS(0): Unable to estimate virtual size
(II) SIS(0): Clock range:  10.00 to 278.18 MHz
(II) SIS(0): Not using default mode "800x600" (vrefresh out of range)
(II) SIS(0): Not using default mode "800x600" (vrefresh out of range)
(II) SIS(0): Not using default mode "800x600" (vrefresh out of range)
(II) SIS(0): Not using default mode "800x600" (vrefresh out of range)
(II) SIS(0): Not using default mode "800x600" (vrefresh out of range)
(II) SIS(0): Not using default mode "800x600" (vrefresh out of range)
(II) SIS(0): Not using default mode "800x600" (hsync out of range)
(II) SIS(0): Not using default mode "640x480" (vrefresh out of range)
(II) SIS(0): Not using default mode "640x480" (vrefresh out of range)
(II) SIS(0): Not using default mode "640x480" (vrefresh out of range)
(II) SIS(0): Not using default mode "640x480" (vrefresh out of range)
(II) SIS(0): Not using default mode "640x480" (vrefresh out of range)
(II) SIS(0): Not using default mode "640x480" (hsync out of range)
(II) SIS(0): Not using default mode "640x480" (hsync out of range)
(II) SIS(0): Not using default mode "1024x768" (vrefresh out of range)
(II) SIS(0): Not using default mode "1024x768" (vrefresh out of range)
(II) SIS(0): Not using default mode "1024x768" (vrefresh out of range)
(II) SIS(0): Not using default mode "1024x768" (vrefresh out of range)
(II) SIS(0): Not using default mode "1024x768" (hsync out of range)
(II) SIS(0): Not using default mode "1024x768" (hsync out of range)
(II) SIS(0): Not using default mode "1280x1024" (unknown reason)
(II) SIS(0): Not using default mode "1280x1024" (unknown reason)
(II) SIS(0): Not using default mode "1280x1024" (unknown reason)
(II) SIS(0): Not using default mode "1280x1024" (unknown reason)
(II) SIS(0): Not using default mode "1600x1200" (unknown reason)
(II) SIS(0): Not using default mode "1600x1200" (unknown reason)
(II) SIS(0): Not using default mode "1600x1200" (unknown reason)
(II) SIS(0): Not using default mode "1600x1200" (unknown reason)
(II) SIS(0): Not using default mode "1600x1200" (unknown reason)
(II) SIS(0): Not using default mode "1600x1200" (unknown reason)
(II) SIS(0): Not using default mode "1600x1200" (bad mode clock/interlace/doublescan)
(II) SIS(0): Not using default mode "1920x1440" (unknown reason)
(II) SIS(0): Not using default mode "1920x1440" (unknown reason)
(II) SIS(0): Not using default mode "1920x1440" (unknown reason)
(II) SIS(0): Not using default mode "1920x1440" (bad mode clock/interlace/doublescan)
(II) SIS(0): Not using default mode "1920x1440" (bad mode clock/interlace/doublescan)
(II) SIS(0): Not using default mode "1920x1440" (bad mode clock/interlace/doublescan)
(II) SIS(0): Not using default mode "2048x1536" (unknown reason)
(II) SIS(0): Not using default mode "2048x1536" (bad mode clock/interlace/doublescan)
(II) SIS(0): Not using default mode "2048x1536" (bad mode clock/interlace/doublescan)
(II) SIS(0): Not using default mode "2048x1536" (bad mode clock/interlace/doublescan)
(II) SIS(0): Not using default mode "2048x1536" (bad mode clock/interlace/doublescan)
(II) SIS(0): Not using default mode "800x480" (vrefresh out of range)
(II) SIS(0): Not using default mode "800x480" (vrefresh out of range)
(II) SIS(0): Not using default mode "1024x576" (vrefresh out of range)
(II) SIS(0): Not using default mode "1024x576" (vrefresh out of range)
(II) SIS(0): Not using default mode "1280x720" (unknown reason)
(II) SIS(0): Not using default mode "1280x720" (unknown reason)
(II) SIS(0): Not using default mode "1280x720" (unknown reason)
(II) SIS(0): Not using default mode "1280x960" (unknown reason)
(II) SIS(0): Not using default mode "1280x960" (unknown reason)
(II) SIS(0): Not using default mode "1280x768" (unknown reason)
(II) SIS(0): Not using default mode "1280x768" (unknown reason)
(II) SIS(0): Not using default mode "1280x768" (unknown reason)
(II) SIS(0): Not using default mode "1400x1050" (unknown reason)
(II) SIS(0): Not using default mode "1400x1050" (unknown reason)
(II) SIS(0): Not using default mode "1152x864" (unknown reason)
(II) SIS(0): Not using default mode "1152x864" (unknown reason)
(II) SIS(0): Not using default mode "1152x864" (unknown reason)
(II) SIS(0): Not using default mode "848x480" (vrefresh out of range)
(II) SIS(0): Not using default mode "856x480" (vrefresh out of range)
(II) SIS(0): Not using default mode "1360x768" (unknown reason)
(II) SIS(0): Not using default mode "1280x800" (unknown reason)
(II) SIS(0): Not using default mode "1280x800" (unknown reason)
(II) SIS(0): Not using default mode "1280x800" (unknown reason)
(II) SIS(0): Not using default mode "1680x1050" (unknown reason)
(II) SIS(0): Not using default mode "1920x1080" (unknown reason)
(II) SIS(0): Not using default mode "1280x854" (unknown reason)
(II) SIS(0): Not using default mode "1280x854" (unknown reason)
(II) SIS(0): Not using default mode "1280x854" (unknown reason)
(--) SIS(0): Virtual size is 1024x768 (pitch 1024)
(**) SIS(0): *Default mode "1024x768" (1024x768) (For CRT device: 65.1 MHz, 48.5 kHz, 60.1 Hz)
(**) SIS(0): *Default mode "1024x576" (1024x576) (For CRT device: 65.1 MHz, 48.5 kHz, 60.1 Hz)
(**) SIS(0): *Default mode "960x600" (960x600) (For CRT device: 41.5 MHz, 37.1 kHz, 60.0 Hz)
(**) SIS(0): *Default mode "960x540" (960x540) (For CRT device: 37.3 MHz, 33.8 kHz, 60.0 Hz)
(**) SIS(0): *Default mode "800x600" (800x600) (For CRT device: 40.0 MHz, 37.9 kHz, 60.3 Hz)
(**) SIS(0): *Default mode "768x576" (768x576) (For CRT device: 35.0 MHz, 35.9 kHz, 60.1 Hz)
(**) SIS(0): *Default mode "720x576" (720x576) (For CRT device: 32.7 MHz, 35.9 kHz, 60.1 Hz)
(**) SIS(0): *Default mode "856x480" (856x480) (For CRT device: 33.9 MHz, 31.7 kHz, 59.8 Hz)
(**) SIS(0): *Default mode "848x480" (848x480) (For CRT device: 33.7 MHz, 31.0 kHz, 60.0 Hz)
(**) SIS(0): *Default mode "800x480" (800x480) (For CRT device: 39.8 MHz, 37.7 kHz, 60.0 Hz)
(**) SIS(0): *Default mode "720x480" (720x480) (For CRT device: 28.3 MHz, 31.6 kHz, 61.0 Hz)
(**) SIS(0): *Default mode "640x480" (640x480) (For CRT device: 25.1 MHz, 31.3 kHz, 59.7 Hz)
(**) SIS(0): *Default mode "640x400" (640x400) (For CRT device: 25.1 MHz, 31.6 kHz, 71.6 Hz)
(**) SIS(0): *Default mode "512x384" (512x384) (For CRT device: 32.6 MHz, 48.5 kHz, 60.1 Hz (D))
(**) SIS(0): *Default mode "400x300" (400x300) (For CRT device: 20.0 MHz, 37.9 kHz, 60.3 Hz (D))
(**) SIS(0): *Default mode "320x240" (320x240) (For CRT device: 12.5 MHz, 31.3 kHz, 60.7 Hz (D))
(**) SIS(0): *Default mode "320x200" (320x200) (For CRT device: 12.5 MHz, 31.3 kHz, 70.9 Hz (D))
(==) SIS(0): DPI set to (96, 96)
(II) Loading sub module "fb"
(II) LoadModule: "fb"
(II) Loading /usr/lib/xorg/modules/libfb.so
(II) Module fb: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.0.0
    ABI class: X.Org ANSI C Emulation, version 0.4
(II) Loading sub module "xaa"
(II) LoadModule: "xaa"
(II) Loading /usr/lib/xorg/modules/libxaa.so
(II) Module xaa: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.2.1
    ABI class: X.Org Video Driver, version 6.0
(II) SIS(0): 2D acceleration enabled
(II) UnloadModule: "vesa"
(II) Unloading /usr/lib/xorg/modules/drivers/vesa_drv.so
(II) UnloadModule: "fbdev"
(II) Unloading /usr/lib/xorg/modules/drivers/fbdev_drv.so
(II) UnloadModule: "fbdevhw"
(II) Unloading /usr/lib/xorg/modules/linux/libfbdevhw.so
(--) Depth 24 pixmap format is 32 bpp
(II) Loading sub module "vbe"
(II) LoadModule: "vbe"
(II) Loading /usr/lib/xorg/modules/libvbe.so
(II) Module vbe: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.1.0
    ABI class: X.Org Video Driver, version 6.0
(II) Loading sub module "int10"
(II) LoadModule: "int10"
(II) Loading /usr/lib/xorg/modules/libint10.so
(II) Module int10: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.0.0
    ABI class: X.Org Video Driver, version 6.0
(II) SIS(0): initializing int10
(II) SIS(0): Primary V_BIOS segment is: 0xc000
(II) SIS(0): VESA BIOS detected
(II) SIS(0): VESA VBE Version 3.0
(II) SIS(0): VESA VBE Total Mem: 32768 kB
(II) SIS(0): VESA VBE OEM: SiS
(II) SIS(0): VESA VBE OEM Software Rev: 1.0
(II) SIS(0): VESA VBE OEM Vendor: Silicon Integrated Systems Corp.
(II) SIS(0): VESA VBE OEM Product: 6325
(II) SIS(0): VESA VBE OEM Product Rev: 1.15.11
(II) SIS(0): Setting standard mode 0x64
(II) SIS(0): RENDER acceleration enabled
(II) SIS(0): Framebuffer from (0,0) to (1023,8046)
(II) SIS(0): Using XFree86 Acceleration Architecture (XAA)
    Screen to screen bit blits
    Solid filled rectangles
    8x8 mono pattern filled rectangles
    8x8 color pattern filled rectangles
    Solid Lines
    Dashed Lines
    Setting up tile and stipple cache:
        32 128x128 slots
        32 256x256 slots
        16 512x512 slots
        32 8x8 color pattern slots
(--) SIS(0): CPU frequency 1533.19Mhz
(II) SIS(0): Benchmarking system RAM to video RAM memory transfer methods:
(--) SIS(0):     Checked libc memcpy()...     273.0 MiB/s
(--) SIS(0):     Checked built-in-1 memcpy()...     260.0 MiB/s
(--) SIS(0):     Checked built-in-2 memcpy()...     56.0 MiB/s
(--) SIS(0):     Checked MMX memcpy()...     263.9 MiB/s
(--) SIS(0):     Checked 3DNow! memcpy()...     258.2 MiB/s
(--) SIS(0):     Checked MMX2 memcpy()...     257.0 MiB/s
(--) SIS(0): Using libc method for aligned data transfers to video RAM
(--) SIS(0): Using libc method for unaligned data transfers to video RAM
(==) SIS(0): Backing store disabled
(==) SIS(0): Silken mouse enabled
(==) SIS(0): DPMS enabled
(II) SIS(0): Using SiS300/315/330/340 series HW Xv by default on CRT2
(II) SIS(0): Initialized SISCTRL extension version 0.1
(II) SIS(0): Registered screen 0 with SISCTRL extension version 0.1
(==) RandR enabled
(II) Initializing built-in extension Generic Event Extension
(II) Initializing built-in extension SHAPE
(II) Initializing built-in extension MIT-SHM
(II) Initializing built-in extension XInputExtension
(II) Initializing built-in extension XTEST
(II) Initializing built-in extension BIG-REQUESTS
(II) Initializing built-in extension SYNC
(II) Initializing built-in extension XKEYBOARD
(II) Initializing built-in extension XC-MISC
(II) Initializing built-in extension SECURITY
(II) Initializing built-in extension XINERAMA
(II) Initializing built-in extension XFIXES
(II) Initializing built-in extension RENDER
(II) Initializing built-in extension RANDR
(II) Initializing built-in extension COMPOSITE
(II) Initializing built-in extension DAMAGE
(II) AIGLX: Screen 0 is not DRI2 capable
(II) AIGLX: Screen 0 is not DRI capable
(II) AIGLX: Loaded and initialized /usr/lib/dri/swrast_dri.so
(II) GLX: Initialized DRISWRAST GL provider for screen 0
(II) XKB: reuse xkmfile /var/lib/xkb/server-B20D7FC79C7F597315E3E501AEF10E0D866E8E92.xkm
(II) config/udev: Adding input device Power Button (/dev/input/event2)
(**) Power Button: Applying InputClass "evdev keyboard catchall"
(II) LoadModule: "evdev"
(II) Loading /usr/lib/xorg/modules/input/evdev_drv.so
(II) Module evdev: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 2.3.2
    Module class: X.Org XInput Driver
    ABI class: X.Org XInput driver, version 7.0
(**) Power Button: always reports core events
(**) Power Button: Device: "/dev/input/event2"
(II) Power Button: Found keys
(II) Power Button: Configuring as keyboard
(II) XINPUT: Adding extended input device "Power Button" (type: KEYBOARD)
(**) Option "xkb_rules" "evdev"
(**) Option "xkb_model" "jp106"
(**) Option "xkb_layout" "jp"
(II) XKB: reuse xkmfile /var/lib/xkb/server-A94739771F15EFE8C025256FFCF9484D873832F7.xkm
(II) config/udev: Adding input device Power Button (/dev/input/event1)
(**) Power Button: Applying InputClass "evdev keyboard catchall"
(**) Power Button: always reports core events
(**) Power Button: Device: "/dev/input/event1"
(II) Power Button: Found keys
(II) Power Button: Configuring as keyboard
(II) XINPUT: Adding extended input device "Power Button" (type: KEYBOARD)
(**) Option "xkb_rules" "evdev"
(**) Option "xkb_model" "jp106"
(**) Option "xkb_layout" "jp"
(II) config/udev: Adding input device Lid Switch (/dev/input/event0)
(II) No input driver/identifier specified (ignoring)
(II) config/udev: Adding input device AT Translated Set 2 keyboard (/dev/input/event4)
(**) AT Translated Set 2 keyboard: Applying InputClass "evdev keyboard catchall"
(**) AT Translated Set 2 keyboard: always reports core events
(**) AT Translated Set 2 keyboard: Device: "/dev/input/event4"
(II) AT Translated Set 2 keyboard: Found keys
(II) AT Translated Set 2 keyboard: Configuring as keyboard
(II) XINPUT: Adding extended input device "AT Translated Set 2 keyboard" (type: KEYBOARD)
(**) Option "xkb_rules" "evdev"
(**) Option "xkb_model" "jp106"
(**) Option "xkb_layout" "jp"
(II) config/udev: Adding input device PS/2 Mouse (/dev/input/event5)
(**) PS/2 Mouse: Applying InputClass "evdev pointer catchall"
(**) PS/2 Mouse: always reports core events
(**) PS/2 Mouse: Device: "/dev/input/event5"
(II) PS/2 Mouse: Found 3 mouse buttons
(II) PS/2 Mouse: Found relative axes
(II) PS/2 Mouse: Found x and y relative axes
(II) PS/2 Mouse: Configuring as mouse
(**) PS/2 Mouse: YAxisMapping: buttons 4 and 5
(**) PS/2 Mouse: EmulateWheelButton: 4, EmulateWheelInertia: 10, EmulateWheelTimeout: 200
(II) XINPUT: Adding extended input device "PS/2 Mouse" (type: MOUSE)
(II) PS/2 Mouse: initialized for relative axes.
(II) config/udev: Adding input device PS/2 Mouse (/dev/input/mouse1)
(II) No input driver/identifier specified (ignoring)
(II) config/udev: Adding input device AlpsPS/2 ALPS GlidePoint (/dev/input/event6)
(**) AlpsPS/2 ALPS GlidePoint: Applying InputClass "evdev pointer catchall"
(**) AlpsPS/2 ALPS GlidePoint: Applying InputClass "evdev touchpad catchall"
(**) AlpsPS/2 ALPS GlidePoint: Applying InputClass "touchpad catchall"
(II) LoadModule: "synaptics"
(II) Loading /usr/lib/xorg/modules/input/synaptics_drv.so
(II) Module synaptics: vendor="X.Org Foundation"
    compiled for 1.7.6, module version = 1.2.2
    Module class: X.Org XInput Driver
    ABI class: X.Org XInput driver, version 7.0
(II) Synaptics touchpad driver version 1.2.2
(**) Option "Device" "/dev/input/event6"
(II) AlpsPS/2 ALPS GlidePoint: x-axis range 0 - 1023
(II) AlpsPS/2 ALPS GlidePoint: y-axis range 0 - 767
(II) AlpsPS/2 ALPS GlidePoint: pressure range 0 - 127
(II) AlpsPS/2 ALPS GlidePoint: finger width range 0 - 0
(II) AlpsPS/2 ALPS GlidePoint: buttons: left right middle
(--) AlpsPS/2 ALPS GlidePoint: touchpad found
(**) AlpsPS/2 ALPS GlidePoint: always reports core events
(II) XINPUT: Adding extended input device "AlpsPS/2 ALPS GlidePoint" (type: TOUCHPAD)
(**) AlpsPS/2 ALPS GlidePoint: (accel) keeping acceleration scheme 1
(**) AlpsPS/2 ALPS GlidePoint: (accel) acceleration profile 0
(**) AlpsPS/2 ALPS GlidePoint: (accel) acceleration factor: 2.000
(**) AlpsPS/2 ALPS GlidePoint: (accel) acceleration threshold: 4
(--) AlpsPS/2 ALPS GlidePoint: touchpad found
(II) config/udev: Adding input device AlpsPS/2 ALPS GlidePoint (/dev/input/mouse2)
(II) No input driver/identifier specified (ignoring)
(II) config/udev: Adding input device Macintosh mouse button emulation (/dev/input/event3)
(**) Macintosh mouse button emulation: Applying InputClass "evdev pointer catchall"
(**) Macintosh mouse button emulation: always reports core events
(**) Macintosh mouse button emulation: Device: "/dev/input/event3"
(II) Macintosh mouse button emulation: Found 3 mouse buttons
(II) Macintosh mouse button emulation: Found relative axes
(II) Macintosh mouse button emulation: Found x and y relative axes
(II) Macintosh mouse button emulation: Configuring as mouse
(**) Macintosh mouse button emulation: YAxisMapping: buttons 4 and 5
(**) Macintosh mouse button emulation: EmulateWheelButton: 4, EmulateWheelInertia: 10, EmulateWheelTimeout: 200
(II) XINPUT: Adding extended input device "Macintosh mouse button emulation" (type: MOUSE)
(II) Macintosh mouse button emulation: initialized for relative axes.
(II) config/udev: Adding input device Macintosh mouse button emulation (/dev/input/mouse0)
(II) No input driver/identifier specified (ignoring)

~~~~@****-my-laptop:~$ ls -al ~/|grep .ICE
-rw-rw-rw-  1 ~~~~ ~~~~  33222 2010-04-12 07:09 .ICEauthority
~~~~@****-my-laptop:~$ ls -l /home
合計 24
drwxrwxrwx 47 ~~~~ ~~~~  4096 2010-04-12 07:21 crab
drwx------  2 root root 16384 2010-04-01 01:18 lost+found
drwxr-xr-x 32 ++   ++    4096 2010-04-11 12:03 xp
~~~~@****-my-laptop:~$ exit
ってとこですかね。
（プライベート事情で、一部伏せています。
～～～～→インストール時に作った管理者権限のある（？）ユーザー
＋＋→後で作ったユーザー
****→コンピューター名の一部
です。）

すいません、英語のページはちょっとしんどいです。
（いまさっき投稿したのは、１０.０４ですが、９.１０でもなっていました。）

書き忘れましたが、今回のケースでは問題の原因の特定に、dmesgが有効かは判りません。
今後のご参考ということで。。

本題に戻ると、複数のX Serverが同じScreen番号で起動するような設定になっていないか確認するのが有効と考えます。
なにかそのような設定変更をした記憶はありませんか。

また、Xが異常終了した際に、変なファイルが/tmpに残ってしまったのかもしれません。
Recovery Modeで起動して、Xが起動していない状態で、/tmp以下を隠しファイル(ドットファイル、ドットディレクトリ)含めて全部消してみてもよいかも知れません。
# 再起動時に/tmpがクリアされたような気もするのですが、念のため。

pc944 による投稿:

/tmpを削除することですが、
$ gksudo nautilus /tmp/
で削除できましたので。

そのやり方だと起動中のgdmやXが使用しているファイルがいたかと思いますが、消せてしまうのですね。逆にびっくり。
その状態で、
$ ls -al /tmp
$ ls -ld /tmp
$ sudo ls -ld /var/lib/gdm
$ sudo ls -l /var/lib/gdm/.ICEauthority
$ sudo file /var/lib/gdm/.ICEauthority
をそれぞれ実行すると、何が表示されますか。

hmatsue による投稿:

複数のX Serverが同じScreen番号で起動するような設定になっていないか確認するのが有効と考えます。
なにかそのような設定変更をした記憶はありませんか。

の件についてはいかがでしょうか。

[参考URL]
http://ubuntuforums.org/showthread.php?t=949750

~~~~@****-my-laptop:/$ sudo ls -ld /var/lib/gdm
[sudo] password for crab:
drwxr-x--- 12 gdm gdm 4096 2010-04-14 21:54 /var/lib/gdm
~~~~@****-my-laptop:/$ sudo ls -l /var/lib/gdm/.ICEauthority
-rw------- 1 gdm gdm 29344 2010-04-14 21:54 /var/lib/gdm/.ICEauthority
~~~~@****-my-laptop:/$ sudo file /var/lib/gdm/.ICEauthority
/var/lib/gdm/.ICEauthority: data
~~~~@****-my-laptop:/$
です。ちなみに、失敗を防ぐためにルートフォルダで作業しています。