I have read that the SUID File Warnings that appear after I run Disk Utility Repair Permissions are not really errors. Will someone please explain what they mean and why they are not errors?
What they mean is that one or more of the Apple software updates modified these files (probably just modifying their permissions settings) without ALSO updating Disk Utility's database of what the correct permissions should be.
Disk Utility is warning you that it detected the modifications made by these updates, and that it is not going to try to second guess the updates and perhaps undo an important change. And thus, if there actually IS anything wrong with the permissions of these specific files (which there isn't), you would have to correct it manually.
Eventually Apple will put out a new update which brings Disk Utility's records back in sync with reality, and these messages will go away.
If you download and apply the full version of the 10.5.1 update, all but one of these SUID file warning messages will go away because the full version happens to include the extra info Disk Utility uses. The ArdAgent file, which was updated by the Remote Management update, will continue to produce that SUID warning.
But you don't HAVE TO re-apply that full 10.5.1. You can, just as Apple says, safely ignore these messages.
--Bob