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Ok, a little brain dead: the short cut I made was still referring to the d: drive as the starting folder.

As for the books that would not scan, there were 5 out of about 1000 books. They were all epubs. I got a meta-data editor to look at them and they all said there was no cover image. I added one, but they still did not scan. Nothing else in the meta-data looked obviously wrong.