Maybe you could load the books in the calibre editor, and use the Check Book feature. Then it'll tell you everything it thinks that's wrong with the book, and it can fix most errors.
Also check the metadata if you haven't already. If you split an omnibus, the splits will retain the metadata of the original, making the seperate books all look the same.
(Oh, scrap. The DC-metadata DiapDealer is mentioning is actually the same stuff is I was trying to tell you to check
Oops.)