Whenever you install a package with the Installer, it saves a "receipt" in /Library/Receipts/. This is an abbreviated copy of the install package, with a list of the files installed and their intended permissions. During the OSX install process, a bunch of receipts are saved for the default OS files. The same thing happens during OS updates.
When doing a permissions repair, those receipts are consulted. This gives Disk Utility the list of permissions for most files - every file that was installed by the Installer. If the receipts have been deleted, then Disk Utility cannot repair permissions because it has no idea what the permissions should be.
Sounds like the receipt packages in that folder have been deleted. If the receipt packages are present, then that folder's permissions may have been reset so as to be unreadable from your current account. Are you trying to repair the disk you are booted from? Reboot from the OSX Install CD/DVD and attempt the permissions repair from there.
It's also possible the Receipts folder has been hit with some directory damage. Do a disk repair.