Thanks for the iPad profile!
I dragged a bunch of ePub files from my Calibre library to iTunes, and I'd say about 30% of them showed up in iBooks with no covers (unlike in Calibre, where they are all perfect) I read somewhere that there is a certain metadata necessary for iBooks to display covers, so I just resaved all my books using the iPad profile, saved them out as ePubs, dragged them to iTunes and...perfect.
Thanks, Kovid!
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