I wrote a QuickLook cover display for Mobipocket long ago. It still work on Kindle books. But I've long forgotten the exact details of how to find the right image for the cover.
But my guess would be that some of the metatdata is wrong. Don't forget that the opf and ncx produced by KindleUnpack aren't really in the MOBI format kindle file. You might want to experiment with the kindleunpack options to get the exact metadata out of the MOBI file without mangling.
I also have a subscription to F&SF. I can't remember noticing bad covers. Give me some issue numbers for good and bad covers and I'll re-download and take a look.
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