Are you sure it is repairing the permissions and not just listing differences that are not actually repaired? It's pretty normal for Disk Utility to just display some differences that it doesn't repair; this has become more common in more recent OS releases. Please try repairing permissions again and seeing if that long list is still there.
I think much of the reason many folks think regular permissions repairing is still needed is because they are just seeing the same reported items, not that any repair is truly being done. I've never quite understood why, but it's normal.
When I just repaired permissions after 10.5.8 combo update, it only actually repaired a dozen irrelevant items in a list ten times as long. In other words, the repairing of permissions wasn't necessary.
