Where is SuperDuper! in all this, Jon? I'm certain we didn't "hose your permissions", since we don't change your permissions at all (and "Repair Permissions" in SuperDuper! is actually done by asking Disk Utility to do it).
Group 501 is the normal "1st user", and it gets created when you create an account (whose ID is also 501).
So... I guess I'm unsure of what you're suggesting SD! did!
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--Dave Nanian
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