What's strange is that the copy script *should* be sharing the /Users folder, not the things inside (that was the change that was made, which works better for a lot of reasons). It sounds like your scripts weren't updated, for some reason.
Here's what I'd suggest: re-download the SuperDuper! image and delete your existing copy of SuperDuper! Drop the new one in its place, and look a the script: it should share /Users, not /Users/* (or .*).
Thanks, and sorry for the trouble.
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--Dave Nanian
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