Strange icon during shutdown...

Does anyone else have a strange icon flash on the display for a fraction of a second during shutdown? I running 10.5.1 on my 15" MBP 2.16 Core Duo and have noticed a real weird icon that only shows up occasionally during shutdown. It usually blinks on and off too fast to really see what it is, but I think it is sort of like the symbol on the command key and has a red X across it. I don't have any issues with the MBP with the exception of some files that Disk Utility is having trouble with when I repair permissions which seems to take a long time. It gets to a point where it says time remaining is less than a minute, but keeps going and going for another 3-5 minutes after displaying this:
Repairing permissions for “Macintosh HD”
Warning: SUID file "usr/libexec/load_hdi" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DiskManagement.framework/Versions/A/Resources /DiskManagementTool" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/Reso urces/Locum" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Install.framework/Versions/A/Resources/runner " has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/readconf ig" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/Admin.framework/Versions/A/Resources/writecon fig" has been modified and will not be repaired.
Warning: SUID file "usr/libexec/authopen" has been modified and will not be repaired.
Warning: SUID file "System/Library/CoreServices/Finder.app/Contents/Resources/OwnerGroupTool" has been modified and will not be repaired.
Permissions repair complete
Anyone seen this before or have any thoughts?

Thanks for the tip.
I did as you suggested and the permissions issue is fully resolved. Never had an issue using the Software Update pane, but I'll file the in my overloaded brain for another time.
I haven't seen the strange icon during shutdown again, but I did identify it as the icon for a piece of software called KeyCue. It shows keyboard shortcuts for the active application by holding down the Command key for about 2 seconds.
Thanks again!

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