I don't have a Nook so this post may be completely irrelevant, but I offer it as another line of enquiry.
I had a similar problem getting my PocketBook 360 to reliably display EPUB cover thumbnails. Sometimes they were OK, sometimes no cover displayed at all and sometimes a random image from the EPUB displayed.
To cut a long story short, I eventually tracked down the problem to the EPUB's
content.opf file <manifest> section and how far down the list the cover item appeared, i.e. the calibre-created line
Code:
<item href="cover.jpeg" id="cover" media-type="image/jpeg"/>
If it was lower than about the 50th item then I didn't get a correct cover thumbnail. If I manually moved it up to be the first item in the manifest then it worked perfectly every time. This is obviously a problem with the PocketBook firmware not calibre.
Apologies if this is a complete red herring for you Nook folks, but I felt I should mention it just in case.
[Edit:] I should also add that resending the tweaked EPUB to the PocketBook was not enough, I had to delete the EPUB from the PocketBook first before resending as the thumbnail extraction seemed to happen only once on initial send.