I just thought about something. Can you upload a book that you already know isn't displaying the cover properly, then eject and unplug your device, then plug the device in again and see if that works?
Failing that, can you find a new book that does work, make a copy of the ePub file, remove it from your device, then run Count Pages on it and if it no longer shows the cover send me both the version before running Count Pages and after running Count Pages?
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