search the forum for "nook color cover" -- there are several threads on the subject.
In short, BN's software is broken and standards compliant epubs still don't show covers sometimes/often.
Many people have had success by doing an epub to epub conversion in Calibre. For the resistant files, some have had success doing a epub to mobi conversion followed by a mobi to epub.
For the final small group of very resistant files, there is a thread with a hand-editing mechanism which the author claims always works.
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