I think I found the answer, and I also think I can fix it... maybe.
Here is what the FAQ said:
My self-made ePub file passes the validity checker, but the table of contents doesn't work when I open it in Stanza iPhone.
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:
I will try this and get you the new file to test.