Seriously silly thing for iTunes to be doing!
Little did he know that when he opened the EPUB file in iTunes, iTunes had the audacity to add a little file to his original EPUB document. No, not only to the EPUB that he copied to iTunes, but also to his original EPUB file. The file is called “iTunesMetadata.plist”. You wont see it unless you look inside an affected EPUB.
To add insult to injury, when Andrew tried to upload his EPUB to the iBookstore, his ebook was rejected because of the aforementioned error! In short, iTunes adds an erroneous file to his EPUB and then Apple says he cant upload the file because of it.
OK, thanks to more information from Andrew, I’ve figured out what the problem was. Although it’s true that iTunes annoyingly adds that iTunesMetadata file to your original EPUB file when you copy the file to iTunes, that’s not what’s causing the invalidation. But if you use iTunes to add a cover to your EPUB, as described in this video by Terry White, and then upload that EPUB to iTunes Producer, that EPUB will not validate and thus will not be accepted into the iBookstore, because the cover image is not properly contained in the OPF file.
via Pigs, Gourds, and Wikis: iTunes invalidates EPUB files for iBookstore.