I have had the same problem with only some of my covers. I had the size set to 314 x 475 for all my covers, but some of them appear as a small image in the top left hand corner.
The only way I found to sort this was to reconvert the epub into another epub in Calibre and that seemed to sort the problem (although a bit inconvenient).
When checking through some others of my epubs, I noticed that when I opened the book in Marvin, the cover art does not appear as the first page (for example it might be the penguin symbol if that is the publisher of the book). And yet the cover art does appear when you view the book as part of a list. I don't know if reconverting the file will sort this as well...
|