The URIs in the ncx file are fairly easy to spot:
Code:
...
<navPoint id="navPoint-6" playOrder="6">
<navLabel>
<text>4</text>
</navLabel>
<content src="Text/Section0007.xhtml"/>
</navPoint>
...
You need to check that these filepaths precisely match what's actually in your epub.
I would recommend you run it through
epubcheck separately, as that will give the line number on which the error occurred.