Disk Utility's Repair Permissions messages that you can safely ignore
http://support.apple.com/kb/TS1448
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired.
Any SUID file basically you can ignore. I have this also after installing Snow Leopard and running software update.
-larco