Preference Repair Oddity

While trying to solve another problem, I have been doing Preference Repairs on my HD regularly and I've noticed something odd. When I run Repair Permissions, I get about 6 screens of messages:

The most frequent messages are the pair Permissions differ on "..." and Repaired "..."

I get 2 or 3 User differs on "..."

And one like this:

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

When I do nothing else but Clear History and run Repair Permissions again, I get about the same number of messages. That seems odd to me. Are the Permissions not repaired? If not, why not. Do they go different right away? Is the Warning message something to worry about?

Maybe this is normal behaviour, or is it? I'm running on a Mac mini (late 2009 model) with Mac OS 10.6.8. I'll be upgrading soon to the new Mac mini and Yosemite but want to make sure things are OK beforehand.