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Disk Warrior may change files, which would - of course - cause those files to be copied. But there's a big difference between having your system lock up as described and copying files.
If your system is locking up there's a low level problem. Patience won't 'fix' it (unless you're waiting for an I/O timeout, again, due to hardware problems).
But, again, this is more correlation than anything else. SuperDuper! is simply copying files...if the hardware or software environment those files are being copied in is unstable, or 'locks up', it will look like SuperDuper! "caused" it (because, after all, we're running), but these high level operations (eg "Copy file a from drive I to drive II") are really performed by the OS, and the lockups are happening at a very low level...
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--Dave Nanian
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