The issue with the Nook and covers has to do with how the Nook expects the cover to be marked in the opf. It looks for a very exact string. Any deviation, even if it still conforms to the EPUB spec, and the Nook will ignore the cover.
calibre when converting to EPUB will be sure to write the cover marker so it will be picked up by the Nook. Simply changing the cover won't rewrite the marker of it is correct (but not in the form the Nook requires).
See
this Sigil bug for more info about this issue.