Would I be right in thinking this was an EPUB3 rather than an EPUB2? The cover page you added via calibre probably contained an image wrapped in an <svg> tag.
For EPUB3s, EpubCheck will show an error if the OPF manifest item for an XHTML file containing an <svg> tag doesn't have a properties="svg" attribute e.g.
Code:
<item href="text/titlepage.xhtml" id="titlepage" media-type="application/xhtml+xml" properties="svg"/>