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I think I may have found a piece of the puzzle. The machine on which I run Calibre is my old desktop, so I've converted it to a sort of server/workstation that I log into via Remote Desktop. On a hunch, I decided to try connecting via VNC instead of Remote Desktop to see if that would affect anything, and interestingly it made Calibre's Nook cover thumbnail generation work properly (see screenshot).
My guess is that the library (or whatever) that Calibre is using to generate the cover thumbnails for the Nook is dependent on some video hardware feature that Remote Desktop doesn't emulate properly. UltraVNC captures the remote computer's video via different methods that apparently don't cause Calibre to malfunction.
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