OK, I did it again today and I think I have more.
Could my hard drive be failing? Corrupted FS? I'm a recent convert so corrupted fat32 and ntfs volumes/partitions are nothing new.
No, those warnings are nothing to worry about....as frustrating as it might be to see them pop up.
When I was running 10.5.x I was getting more and more of those, each time I'd add something, updated software, etc
Just look at it as a reporting problem with the OS X, so to speak, it has something to do with not recognizing old against new receipts or something like that.
When I upgraded to snow leopard, if I run repair permissions a 2nd time when I get these messages, for some reason I see that they have all disappeared.
The warnings that I got though when I upgraded, after restoring from backup were ACL found but not expected warnings.... which I managed to stop coming up, and 2 suid file warnings, which I've learned to accept.
The long and short is that Apple says that all these warning are safe to ignore.
It is just good practice to run repair permissions periodically, and as long as your system is running fine, if it ain't broke, don't try to fix it