Does your TOC look like this?

<item id="ncx" href="toc.ncx" media-type="text/xml"/>

If so, the "media-type" is incorrect. It should read:

<item id="ncx" href="toc.ncx" media-type="application/x-dtbncx+xml"/>

The fact that epubcheck doesn't validate this requirement in the spec is a bug in epubcheck itself:

http://code.google.com/p/epubcheck/issues/detail?id=21