Hm -- that's really strange, and we haven't had it reported before. SuperDuper! repairs permissions *with* Disk Utility (by calling the same low-level tool), so it certainly shouldn't slow down the system.
I think what Jonas suggested there is a good thing to do: check to see if there's some other program on the system that's taking time. Are you running anything 'unusual' on your system, or low-level, like Norton AntiVirus or the like?
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--Dave Nanian
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