Originally Posted by vootie
The thing is, there is no cover.html file in the epub, despite my specifying a cover image in InDesign.
That's because there is no proper "cover" definition in the ePub format, nothing wrong with your file, it's just not in the specification. The use of a <meta name="cover"> tag is an ad-hoc solution that makes sense and may work with some reading software, but there's nothing in the ePub spec that says it must work, it's only a custom metadata field that can be added (and there's no way Sigil can know the image is referenced there, because <meta> tags can contain any text, not necessarily a file id, it's the reading software who will interpret it one way or another).
You could add an XHTML file that uses the cover image, or just ignore the validator warning, it doesn't make the ePub file invalid (it would be invalid if the image did not appear in the manifest, though).