Oh, actually, it might be the import. I didn't realise the Calibre viewer could open MOBI files (
), but I accidentally clicked on that link when I was trying out one of the 'good' ones as an example, and realised it could. The MOBI file opened in the E-book Viewer, and looks, as far as I can see, just like the EPUB one - there's a slight difference in the page numbers, but all the chapter headings look the same.
Anyhoo, I imported one of the 'bad' files, and tried out that MOBI and it's one, apparently blank, page. When I convert it, I then get the cover, followed by one blank page. 'Sweird!