Odd warning when Repairing Permissions

I know that since OSX, repairing permissions is not something often talked about. But I figure it must be still useful or Apple would have dropped it from its OS updates.

I've been having a few odd things going on with my computer, mainly in Mail, so I decided to run Repair Permissions. This is what I got:

"Warning: SUID file "System/Library/CoreS...as been modified and will not be repaired."

What the heck does this mean and how was it modified? I have NEVER gone into Terminal Mode and done anything to my System Software.

It fixed a couple of minor things regarding my printers.

What gives?