I have this same problem... Did any solution work for you? I'm new to Calibre, and I added four books to the software on my desktop, fixed their metadata, then transferred them to the Nook Color. Of the four, only one had it's cover image show up. Thinking that I had made a mistake, I redownloaded all the covers for the epub books, re-"converted" them, deleted the original four off my nook color, and re-transferred the epub books to my nook color. This time, a different one showed it's cover, and the others showed the generic cover. I started to think it may be a nook problem, then I came across this forum post...
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