Have you tried uploading it to any other publisher, or just Apple? If you're having trouble with other publishers as well, can you send me the ePub file and we'll run it through our validation checker to find any errors.
If it seems to be only Apple, can you check the size of your book cover. If you go to the Book Details section of your book where you uploaded the cover, you'll see there's a little note there if you hover over the ? icon with details about the sizing of the cover image Apple iBooks will allow. For quick reference, it cannot exceed 1600x2400 or a total of 4 million pixels.