I just uploaded 698 epubs to Calibre Companion on a new Nook HD using the wireless connection to Calibre. Every single cover shows up fine. So, seacity, if you can't figure out what the issue is based on the suggestions given so far, I'd be happy to try to troubleshoot the problem if you pm me with a download link to one of the epubs you are having an issue with. Since I have virtually the same hardware and software you are using, I can try out your file and see if it's working for me. That may help pinpoint where the problem lies.
--Pat
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