This is but one of several ways Leopard's permissions repair gets it wrong. (more >
here<)
In your case (or, if anyone enjoys repairing permissions and wants it to report accurately
then), running the 10.5.5
Combo Update will probably get things back in sync. Basically...
some delta updates don't seem to be properly updating the info in /Library/Receipts/boms
so Disk Utility
thinks there's a problem (when it shouldn't).