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The only thing I can guess is a permissions problem, but that would be fixed by the uninstall and deleteing of the folder. So yes, something is being missed, but I'm afraid with your imperfect description of the problem I'm at a loss to say what's going wrong.
You might try as Kovid suggested before... forget save to disk, just copy the Mac library directory onto your USB drive, then copy the library folder from your USB drive onto Windows (after deleteing the old library folder), and starting calibre from the command line with the path to the new library. But you'd need to understand what the path was on your PC in order to do that.
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