I haven't worked with Nook Press, but I wouldn't be surprised if something like that ignored the HTML cover entirely. Do you have an image cover item in your manifest? e.g.
Code:
<metadata xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:opf="http://www.idpf.org/2007/opf">
...
<meta name="cover" content="cover-image"/>
</metadata>
<manifest>
...
<item id="cover-image" href="OEBPS/Images/7mm_1_high.jpg" media-type="image/jpeg"/>
...
</manifest>