I have a Mac Pro running Snow Leopard 10.6.5. When I repair permissions, there are about a dozen items that are listed as repaired. But if I repeat the process, either immediately or a day later, the same list is repaired all over again. What gives?
I can say with some confidence that the messages you see repeated time and again contain the word Java. You might also see Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/ Contents/MacOS/ARDAgent” has been modified and will not be repaired.
Apple tells us “don’t sweat it” in its KnowledgeBase article, Mac OS X: Disk Utility’s Repair Disk Permissions messages that you can safely ignore. After listing scads of these messages, the document ends with:
You can safely ignore these messages. You can also usually ignore any “ACL found but not expected…” message. These messages can occur if you change permissions on a file or directory. These messages are accurate but are generally not a cause for concern.