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When Calibre sends a book to the Nook, I believe that it sends the entire set of files that it has in the subdirectory for that book; it may even send the entire subdirectory as a subdirectory (I forget). Perhaps there is something about the way you are doing the Mobi conversion that makes it necessary to send all the Calibre files (e.g. cover.jpg, metadata files, etc), instead of just the .epub file (which is usually all you need).
I think you should play around with the Mobi conversion options (there are many, if I remember correctly).
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