When you downloaded it, did you then run a conversion on the ebook? When you first download a cover, it's kept as a separate file and displayed with your metadata. But it's not in the book itself until you until you convert the ebook - even if it's just to-and-from the same format.
Also, are you reading the book in the Calibre book viewer or on your reader?
I *think* there's a setting so that when you have updated metadata then send it to your reader, it automatically reconverts the book, but I'm not sure about that.
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