When you go to Preferences => Metadata download, which of the metadata source are checked? You might also want to highlight/configure each of the sources (for me, that means turning off ratings and tags as downloadable metadata). Other things are if you use the Kindle Hi-Res covers plugin, it works best if you have the mobi-asin in the book IDs list. If the search returns multiple images, it should show you a box with the existing and downloadable covers so you can select which one you want.
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