The only time I've seen this happen is when the book has no cover defined. Typically a cover is the first page, but the device requires a cover to be explicitly defined. Almost all books have this and I just need to tweak a value. Are you able to send me any of the books that don't have covers? If not, can you open a book and send me the file that has the extension '.opf'? An ePub is just a fancy ZIP file, so if you add '.zip' as the extension to any book you can open it as a ZIP file and copy the OPF file out that way.
After that, can you try converting one book with calibre to ePub format and make sure to tell calibre to make a cover, see if that works when uploaded?
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