I had the same problem. I first noticed it with free Tor books. With those, I had downloaded the mobi format and sent it to my kindle email. No book cover. The next month a free book had a 32 mb file size in mobi, but half that in epub. Since the download speed was very slow that day, I downloaded the epub and converted it to mobi. That file did have a cover when emailed to my kindle. I then removed the cover less books from my Amazon account, deleted the mobi files from my computer, converted epub to mobi for 5 books and sent them to my kindle. They all now had a cover.
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