[jlmwrite]

I've been home the past few days with a nasty upper respiratory infection, so in between reading and blowing my nose incessantly, I decided to lick this problem.

Short answer: I deleted my entire library off the NC from inside Calibre, rebooted, then reinstalled my entire library to the NCs main memory. Every cover shows properly, and books added after that are all where they should be.

Long answer: Whatever indexing/caching method the NC uses was getting confused with the additions/deletions, plus the multiple copies of that last batch of books I'd installed to test Aldiko were affecting things. Some of the problems that cropped up -- Some covers were showing in certain library views but not in others. The books that I had added weren't showing as 'most recent' but instead were showing up at the very end of the library, and being marked by the library as "unknown date" even though the books themselves had the proper date in them. The more I deleted and added those books, the worse the problems.

My assumption is that the multiple copies of that last batch of books on my SD card (from using Aldiko) confused the NC. I used Calibre to delete all copies from the SD card and deleted my entire library from the NC's memory. I rebooted for good measure, reinstalled all my books, and every one of my issues disappeared -- including the few sideloaded covers that sometimes showed and sometimes didn't.

FYI -- When I reloaded all 786 books, it only took the NC a few minutes to repopulate the library. I did have to press the refresh button inside the library four or five times yet it took less than 3 minutes for all my books to show. Compare that to when I sideloaded 400 books onto my Kindle 3, and it indexed overnight.

Since I reloaded my library, I've not had a single problem. I've purchased two more books, and sideloaded another 6 or 7 older books on two separate days. I'm happy again!