I'm sure you've already tried this but maybe......I put a number of eReader and Adobe pdfs onmy Nook and it didn't see them either. Then I remembered in the manual, one very small section, that states you must do the eject through "My Computer" to get the Nook to recognize the new data. I went back on my computer and did the eject per their instructions and everything is fine. Suddenly the Nooks saw the books uploaded.
You've probably already done that, but I thought it was worth a mention.
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