Clean Install 10.6 to Cure broken disk permissions?

My wife's 2006 MacBook has bogged down horribly over time. When I checked it with Disk Utilities, Disk Verification reports it is fine, but I found dozens of faulty Disk Permissions, including an especially ominous one:

"Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired."

So I backed-up up her data, both using Time Machine and copying the files using the Finder. I erased and formatted the HD, ran my SnowLeopard System Install DVD, and restored her data via Time Machine [knowing this might possibly bring some of the junk back, as it was not a truly 'clean install'.

The broken permissions were there, in the new SnowLeopard system on the erased HD. I ran a pass of Repair Disk Permissions; it indicated it repaired each one except the one above, but when I ran Verify Disk Permissions again, dozens of broken permissions were listed.

So, I re-erased the HD, installed only SnowLeopard from the DVD and did the software updates via System Preferences. At this point I have NOT restored any of my wife's files or data - nothing. And the broken permissions are back again.

Any idea what is wrong? I am baffled? HELP!

Are you recommending that I can just ignore all of them, or just the one you know is on the list?