Update: just did a Combo Update to 10.7.2 and the aforementioned warning no longer appears after a Permissions Repair.
That sounds promising, and is precisely how the permanent fix should come (if/when it comes). As it is, any given update has the
potential to permanently (or temporarily
appear to) fix this bug. So your recent joy may just be a fluke... meaning: the forthcoming 10.7.3 update (or any other update such as Security, Java, etc.,) could easily introduce more changed items, about which Disk Utility might once again act totally oblivious. Time will tell.
If Apple has indeed squashed the bug, i hope they'll release a 10.6.9 update to clear up Snow Leopard as well.