That's one of the warnings that you can safely ignore.
Mac OS X: Disk Utility's Repair Disk Permissions messages that you can safely ignore. You will get that message every time that you repair permissions; it happens to me too.
Ignore it and have a Happy New Year!

How often do you repair permissions? I had heard it wasn't necessary any more.
QUOTE
How often do you repair permissions? I had heard it wasn't necessary any more.
I always operated under the belief that it's easier to ask for forgiveness than permission...
Seriously, the non-problematic 'warnings' make it more frustrating than helpful to perform this function. Many utilities, such as SuperDuper, can perform this task during their normal operation and you may be doing that daily, anyway. I basically follow the same 'schedule' as Jon; when I think about or have some kind of minor problem. 
With Apple's seeming obsession for frequent notifications of updates, I don't understand why they can't/won't make this utility more machine/OS specific. It would certainly make their systems look more stable and reliable than publishing a document saying, basically:QUOTE
Don't worry about what our own utility is telling you. It really doesn't know what it's talking about. OTOH, there may be something it's telling you that is important, we just don't have time to fix the reporting mechanism.
And thanks for buying our products, BTW!
That list was updated that list a little over six months ago...