[dnanian]

Well, Ulf, as I've said elsewhere, we've never seen a case where SuperDuper! didn't copy a file it was supposed to copy. So I don't think something "bad" happened here.

Rather, I'd guess that one of the files that's being deliberately ignored is quite large. Unusually so. I can't verify that from here, but you can check for yourself by examining the copy script you're using. Every file that's being treated specially is there, and you can see if any are large on your machine.

One distinct possibility: a folder in /Volumes that has data in it, even when no drive is attached...