Calibre uses the <guide> section of the OPF to identify the cover page. The page should also be in the <manifest> and its "id" listed as the first item in the <spine> section.
Right click on the epub in Calibre and use the Tweak Book option to view the OPF file. See if it looks like this:
<manifest>
<item href="filename.html" id="cover" media-type="application/xhtml+xml"/>
.
.
.
</manifest>
<spine>
<itemref idref="cover"/>
.
.
.
</spine>
<guide>
<reference href="filename.html" title="Cover" type="cover"/>
.
.
.
</guide>