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Just because an epub passes FlightCrew and EpubCheck validation doesn't mean it might not include something that the Kindlegen conversion process doesn't support/can't handle.
As Doitsu suggested, do a conversion of the epub locally (with the very latest Kindlegen/Kindle Previewer) to see what might be going on. I'd recommend uploading kindlegen output instead of epubs anyway. That way you know before uploading that there may be an issue.
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