Permissions and Strange behaviours

[Avro]

I have been having some problems with Snow Leopard, SBBD, freezes, disappearing dock, I get 2,000 changes in the dock notifications. My F keys don't work. Same problems on Mac Pro and MacBook. Using Leopard on a separate drive to post this.

I tried to repair permissions with Drive Genius 2 and got this message:

Repairing permissions...
Started verify/repair permissions on disk2s2 Mac One
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired
Warning: SUID file "System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/Resources/Locum" has been modified and will not be repaired
Finished verify/repair permissions on disk2s2 Mac One

Any idea what could be wrong?