Problem happens without any program running, maybe (if below system.log info does not assist) I can just turn it on, leave it alone with nothing opened after startup, and copy and paste the log info then. In the meantime, I believe the following is from the system.log at that time:
Oct 5 19:59:48 Nicholas-Fords-MacBook.local WindowServer[123]: CGXSetWindowTransform: Invalid window 0x1a4
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSSetWindowTransformAtPlacement: Failed
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSSetWindowListGlobalClipShape: Invalid window 0x1a4
Oct 5 19:59:48 --- last message repeated 1 time ---
Oct 5 19:59:48 Nicholas-Fords-MacBook.local WindowServer[123]: CGXSetWindowTransformList: Invalid window 0x1a4
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSSetWindowTransformsAtPlacement: Failed
Oct 5 19:59:48 Nicholas-Fords-MacBook.local WindowServer[123]: CGXSetWindowTransform: Invalid window 0x1a4
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSSetWindowTransformAtPlacement: Failed
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSSetWindowListGlobalClipShape: Invalid window 0x1a4
Oct 5 19:59:48 --- last message repeated 1 time ---
Oct 5 19:59:48 Nicholas-Fords-MacBook.local WindowServer[123]: CGXSetWindowTransformList: Invalid window 0x1a4
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSSetWindowTransformsAtPlacement: Failed
Oct 5 19:59:48 Nicholas-Fords-MacBook.local WindowServer[123]: CGXSetWindowTransform: Invalid window 0x1a4
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSSetWindowTransformAtPlacement: Failed
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSGetWindowTags: Invalid window 0x1ac
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSGetWindowTags: Invalid window 0x1ab
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSGetWindowTags: Invalid window 0x1aa
Oct 5 19:59:48 Nicholas-Fords-MacBook.local Dock[198]: CGSGetWindowTags: Invalid window 0x1a9
Oct 5 20:00:20 Nicholas-Fords-MacBook.local Locum[369]: Connection with distnoted server was invalidated
Oct 5 20:00:20 Nicholas-Fords-MacBook.local coreaudiod[142]: AudioComponentPluginLoader: can't create bundle: A52Codec.component -- file://localhost/Library/Audio/Plug-Ins/Components/
Oct 5 20:00:21 Nicholas-Fords-MacBook kernel[0]: Sandbox: sandboxd(370) deny mach-lookup com.apple.coresymbolicationd
Oct 5 20:00:21 Nicholas-Fords-MacBook.local sandboxd[370] ([142]): coreaudiod(142) deny file-read-data /Library/Audio/Plug-Ins/Components/A52Codec.component
Oct 5 20:00:21 Nicholas-Fords-MacBook.local sandboxd[370] ([142]): coreaudiod(142) deny file-read-metadata /Library/Audio/Plug-Ins/Components/A52Codec.component/Contents
Oct 5 20:00:21 Nicholas-Fords-MacBook.local sandboxd[370] ([142]): coreaudiod(142) deny file-read-metadata /Library/Audio/Plug-Ins/Components/A52Codec.component
Oct 5 20:02:33 Nicholas-Fords-MacBook kernel[0]: considerRebuildOfPrelinkedKernel prebuild rebuild has expired
Oct 5 20:02:33 Nicholas-Fords-MacBook kernel[0]: USBMSC Identifier (non-unique): 001CC0EC34B2EC21163201CB 0x930 0x6545 0x100
Oct 5 20:02:38 Nicholas-Fords-MacBook.local fseventsd[53]: check_vol_last_mod_time:XXX failed to get mount time (25; &mount_time == 0x10709b528)
Oct 5 20:02:38 Nicholas-Fords-MacBook.local fseventsd[53]: log dir: /Volumes/16GB USB/.fseventsd getting new uuid: 5EF6593B-1339-41B1-B18D-FDD07C41EC43
Oct 5 20:03:32 Nicholas-Fords-MacBook.local Locum[397]: Connection with distnoted server was invalidated
Oct 5 20:03:39 Nicholas-Fords-MacBook.local Window Tidy[250]: Starting new group
Oct 5 20:03:39 Nicholas-Fords-MacBook.local Window Tidy[250]: Setting window index 0. Now 1 windows
Oct 5 20:03:39 Nicholas-Fords-MacBook.local Window Tidy[250]: Starting new group
Oct 5 20:03:39 Nicholas-Fords-MacBook.local Window Tidy[250]: Setting window index 1. Now 2 windows
Oct 5 20:03:39 Nicholas-Fords-MacBook.local Window Tidy[250]: Starting new group
Oct 5 20:03:39 Nicholas-Fords-MacBook.local Window Tidy[250]: Setting window index 2. Now 3 windows
Oct 5 20:03:39 Nicholas-Fords-MacBook.local Window Tidy[250]: Starting new group
Oct 5 20:03:39 Nicholas-Fords-MacBook.local Window Tidy[250]: Setting window index 3. Now 4 windows
Oct 5 20:03:51 Nicholas-Fords-MacBook.local Locum[398]: Connection with distnoted server was invalidated
Oct 5 20:06:04 Nicholas-Fords-MacBook kernel[0]: 2.4.4 m168efe17
Oct 5 20:06:42 Nicholas-Fords-MacBook kernel[0]: 2.4.4 m168efe17
Oct 5 20:06:42 Nicholas-Fords-MacBook.local com.apple.SecurityServer[15]: Succeeded authorizing right 'system.volume.removable.unmount' by client '/System/Library/CoreServices/Finder.app' [199] for authorization created by '/System/Library/CoreServices/Finder.app' [199] (100013,0)
Oct 5 20:06:42 Nicholas-Fords-MacBook.local com.apple.SecurityServer[15]: Succeeded authorizing right 'system.volume.removable.unmount' by client '/usr/sbin/diskarbitrationd' [21] for authorization created by '/System/Library/CoreServices/Finder.app' [199] (100002,0)
Oct 5 20:06:44 Nicholas-Fords-MacBook.local com.apple.SecurityServer[15]: Succeeded authorizing right 'system.volume.removable.unmount' by client '/System/Library/CoreServices/Finder.app' [199] for authorization created by '/System/Library/CoreServices/Finder.app' [199] (100013,0)
Oct 5 20:06:44 Nicholas-Fords-MacBook.local com.apple.SecurityServer[15]: Succeeded authorizing right 'system.volume.removable.unmount' by client '/usr/sbin/diskarbitrationd' [21] for authorization created by '/System/Library/CoreServices/Finder.app' [199] (100002,0)
Oct 5 20:06:57 Nicholas-Fords-MacBook kernel[0]: 2.4.4 m168efe17
Oct 5 20:07:04 --- last message repeated 1 time ---
Oct 5 20:07:04 Nicholas-Fords-MacBook com.apple.launchd[1] (com.apple.coremedia.videodecoder[396]): Exit timeout elapsed (20 seconds). Killing
Oct 5 20:07:21 Nicholas-Fords-MacBook.local Google Chrome Helper EH[423]: Unsure about the internals of CFAllocator but going to patch them anyway. If there is a crash inside of CFAllocatorAllocate, please report it at http://crbug.com/117476 . If there is a crash and it is NOT inside of CFAllocatorAllocate, it is NOT RELATED. DO NOT REPORT IT THERE but rather FILE A NEW BUG.
Oct 5 20:12:07 Nicholas-Fords-MacBook.local WindowServer[123]: Created shield window 0x1f6 for display 0x04272d80
Oct 5 20:12:07 Nicholas-Fords-MacBook.local WindowServer[123]: Created shield window 0x1f7 for display 0x042480e5
Oct 5 20:12:07 Nicholas-Fords-MacBook.local WindowServer[123]: device_generate_desktop_screenshot: authw 0x0(0), shield 0x0(0)
Oct 5 20:12:07 Nicholas-Fords-MacBook.local WindowServer[123]: device_generate_lock_screen_screenshot: authw 0x0(0), shield 0x0(0)
Oct 5 20:12:07 Nicholas-Fords-MacBook.local WindowServer[123]: device_generate_desktop_screenshot: authw 0x0(0), shield 0x0(0)
Oct 5 20:31:43 Nicholas-Fords-MacBook.local WindowServer[123]: handle_will_sleep_auth_and_shield_windows: no lock state data
Oct 5 20:31:49 --- last message repeated 1 time ---
Oct 5 20:31:49 Nicholas-Fords-MacBook.local iTunes[301]: 2012-10-05 08:31:49.998406 PM [AVSystemController] Stopping AirPlay
Oct 5 20:31:50 Nicholas-Fords-MacBook.local Dock[198]: CGSGetWindowTags: Invalid window 0x216
Oct 5 20:31:50 Nicholas-Fords-MacBook.local Dock[198]: CGSGetWindowTags: Invalid window 0x215
Oct 5 20:31:50 Nicholas-Fords-MacBook.local Dock[198]: CGSGetWindowTags: Invalid window 0x214
Oct 5 20:31:50 Nicholas-Fords-MacBook.local Dock[198]: CGSGetWindowTags: Invalid window 0x213
Oct 5 20:32:22 Nicholas-Fords-MacBook.local Google Chrome Helper[443]: Unsure about the internals of CFAllocator but going to patch them anyway. If there is a crash inside of CFAllocatorAllocate, please report it at http://crbug.com/117476 . If there is a crash and it is NOT inside of CFAllocatorAllocate, it is NOT RELATED. DO NOT REPORT IT THERE but rather FILE A NEW BUG.
Oct 5 20:32:22 Nicholas-Fords-MacBook.local Google Chrome Helper[444]: Unsure about the internals of CFAllocator but going to patch them anyway. If there is a crash inside of CFAllocatorAllocate, please report it at http://crbug.com/117476 . If there is a crash and it is NOT inside of CFAllocatorAllocate, it is NOT RELATED. DO NOT REPORT IT THERE but rather FILE A NEW BUG.
Oct 5 20:32:22 Nicholas-Fords-MacBook.local Google Chrome Helper[443]: bootstrap_look_up2 failed with 0x44c
Oct 5 20:32:22 Nicholas-Fords-MacBook.local Google Chrome Helper[443]: CGSLookupServerRootPort: Failed to look up the port for "com.apple.windowserver.active" (1100)
Oct 5 20:32:22 Nicholas-Fords-MacBook.local Google Chrome Helper[445]: Unsure about the internals of CFAllocator but going to patch them anyway. If there is a crash inside of CFAllocatorAllocate, please report it at http://crbug.com/117476 . If there is a crash and it is NOT inside of CFAllocatorAllocate, it is NOT RELATED. DO NOT REPORT IT THERE but rather FILE A NEW BUG.
Oct 5 20:32:24 Nicholas-Fords-MacBook.local Google Chrome Helper[446]: Unsure about the internals of CFAllocator but going to patch them anyway. If there is a crash inside of CFAllocatorAllocate, please report it at http://crbug.com/117476 . If there is a crash and it is NOT inside of CFAllocatorAllocate, it is NOT RELATED. DO NOT REPORT IT THERE but rather FILE A NEW BUG.
Oct 5 20:32:26 Nicholas-Fords-MacBook.local Google Chrome Helper[446]: bootstrap_look_up2 failed with 0x44c
Oct 5 20:32:26 Nicholas-Fords-MacBook.local Google Chrome Helper[446]: CGSLookupServerRootPort: Failed to look up the port for "com.apple.windowserver.active" (1100)
Oct 5 20:32:51 Nicholas-Fords-MacBook.local Google Chrome Helper[446]: Failed to look up domain bootstrapper during domain extension: 0x44c
Oct 5 20:32:51 --- last message repeated 12 times ---
Oct 5 20:32:51 Nicholas-Fords-MacBook.local Google Chrome Helper EH[448]: Unsure about the internals of CFAllocator but going to patch them anyway. If there is a crash inside of CFAllocatorAllocate, please report it at http://crbug.com/117476 . If there is a crash and it is NOT inside of CFAllocatorAllocate, it is NOT RELATED. DO NOT REPORT IT THERE but rather FILE A NEW BUG.
Oct 5 20:32:55 Nicholas-Fords-MacBook.local Google Chrome Helper[446]: Failed to look up domain bootstrapper during domain extension: 0x44c
Oct 5 20:33:18 Nicholas-Fords-MacBook kernel[0]: CODE SIGNING: cs_invalid_page(0x1000): p=449[GoogleSoftwareUp] clearing CS_VALID
Oct 5 20:39:40 localhost bootlog[0]: BOOT_TIME 1349483980 0