In general, we suggest that you not use the computer while you're backing up. That way, your backup will contain what you expect it to. In addition, you won't end up trying to write something at the exact same time SuperDuper! is trying to back it up.
It's not possible, though, to stop everything on the computer and back it up (unless you boot from something else). OSX has lots and lots of things running at the same time.
So -- minimize your use, and that should be fine.
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--Dave Nanian
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