Hm... what you did should certainly work OK, as long as you're running a recent version of SuperDuper! (meaning 1.5 or later). I don't know of any case where permissions would get changed or cloned improperly.
In this case, I'd need to see the permissions for the involved files and directory. Unfortunately, since you've moved Preferences already we can't use that as an example, but if you have another case that'd help. Do an ls -l on both the file that's failing and its enclosing folder.
Thanks -- we'll hopefully be able to figure this out.
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--Dave Nanian
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