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I have had this before and it is exactly as mentioned above, unless the cover is already embedded in the ePub, Calibre is just showing you the cover from the jpeg file in the book directory (which doesn't get transferred over)
When I make any changes to a book in Calibre I always do a convert (ePub to ePub) , this embeds the cover into the ePub file so it transfers to the reader
try it on one of your problem books as a test and hopefully it should fix the issue
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