By 'meddling' I meant hand-tweaking the xhtml code after calibre conversion to ePub. Books that I produce with calibre have zero validation errors unless I've manually introduced one with Notepad++ editing, (usually by missing a closing xml tag). The behaviour is then similar to what you describe.
Have you looked at the reported errors? If they can be clearly shown to be a calibre bug then I'm sure the developers would work on a fix.
Are you able to make a small sample of the book which demonstrates the problem? You could post this if copyright allows. What format was it converted from?
Last edited by Agama; 01-17-2013 at 08:22 AM.