Hello tas,
My experience is with older NOOKs (the Simple Touch and the Glowlight - the white one). What I learned about them is that they store cover images in a file called .docThumbs. The NST makes a copy of the cover image of each book loaded onto it. It uses these images for thumbnails displayed on the library shelves, and stores those images in .docThumbs. So if that file has accidentally been deleted, you will get the generic blank cover thumbnails.
Also, those older NOOKs look for a file called "cover.jpg" (or cover.something, anyway) to use for the thumbnail image. If your book uses a cover image with a different name, you won't get a thumbnail picture on your library shelves, just the blank white rectangle with the title and author.
Hopefully these clues can give you some leads to investigate!
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