Originally Posted by cybmole
could be - I don't know how to edit .ofp - usually I just delete unwanted toc, dedication, epigraph... XHTML entries...
It's possible that's your problem, then. If you're doing it via Sigil, I expect Sigil does some automatic opf-tidying-up as you remove chunks and save the changes. But I don't know it well enough to know in detail exactly what it does and doesn't clean up.
The <manifest> is a list (id, url, media-type) of all the files in the epub,
the <spine> is an ordered list of ids of the html files which will be displayed when you read the epub,
and the <guide> is... I'm not sure what it's purpose is in an epub but I think the items in there are used by Kindle formats.