I did a complete wipe and install of 10.6 this weekend. After moving my personal files back and tweaking other things like Bookmarks, etc., I ran the Repair Disk Permissions routine and got this same message. I'm used to seeing innocuous errors here however, I did a quick Google search and found this article right off the bat:
http://www.macosxhints.com/article.php?story=20080620052233168 ==> "+ARDAgent runs when you use Screen Sharing in 10.5, and if you've enabled Remote Management in the System Preferences panel, but this exploit actually works when ARDAgent isn't running.+"
Even though this article was written in June of 2008, it refers to a security hole associated with this file "ARDAgent.app" and seeing the Apple Support Article #TS1448 - then the words, messages that you can safely ignore... I'm not so sure. This article refers to release 10.5 and not 10.6 and while the previous article from June last year may be relating to yet an earlier 10.5 release, its still gives me pause for concern. I've seen many times when a previous bug recurs after a new release due to an oversight but I just don't know.
I'm not one that can simply dismiss an alert because Apple says "you can safely ignore" particularly when previously there was a security hole associated with this very file.
We all know that Mac's are very secure and reliable however, I'm concerned none the less.