*How*, exactly, are you adding the cover to the epub? Better yet, why not provide the actual file you're having trouble with.
Another idea, if you have an problematic epub, is to try an Epub to Epub conversion in Calibre. Calibre has built up a vast repertoir of common pitfalls it 'fixes' on the fly when doing this. If course, GIBO still applies, so results may vary.
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