I am not sure, fix permissions is a two sided blade. It cuts both ways. The items in question should never be changed from what they originally were. Really, repair permissions is suppose to fix permissions issues with your home directory nothing else really.

It doesn't have the power (and I think it never should by design) to alter anything in a Unix level directory like /usr, or /System, or /Library

Apple has this document:

Mac OS X 10.5: Disk Utility's Repair Disk Permissions reports issues with SUID files

I haven't read through this whole post so I'm not sure if you're running Leopard?

Regarding your specific Warnings, they aren't listed in that Apple doc so I can't say 100% for sure that they are safe to ignore ... someone more cluey or simply better informed will need to step in. :)

VirtualTracy,

Thanks for the link to the SUID page. Good advice. It said it is safe to ignore the warnings.