Is this with the Kobo Glo? If so, it uses the first page of the book as the cover. It generates the page as needed and stores the images for later use. Unless the book is on the SD card, in which case the image is generated each time it is needed.
The above means that if the first page of the book displays OK, the cover should be OK.
If you convert the book to put a new cover into it, or use Polish books, you need to resend the book to the Glo. If the Glo has already generated the covers, they are not updated. For the recent versions of the calibre, from 0.9.21 I think, the covers are removed on the device when the book is resent. That allows them to be regenerated.
If you have a book that is still not working, I would like to see it. Or grab a book from the library here and test it. If it doesn't work I can get a copy and test it as well.
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