Did you declare the "XHTML" or "HTML" containing the "cover" in the "GUIDE" section of the OPF?
Code:
<guide>
<reference href="Text/coverpage.xhtml" title="Cover" type="cover" />
</guide>
AFAIK, the "cover" used by Kindlegen is from the
Code:
<meta content="Cover.jpg" name="cover" />
OPF so if the XHTML containing the "cover" image is not declared in the "GUIDE" area Kindle will treat it as a normal page.