I found that decreasing the size of the library loaded on the SD card solved the "disappearing bookshelf" problem. Try limiting the number of books to less than 200. If all works well, you can try adding more.
I also found that having a large number of books on the SD card dramatically slowed the system's performance when browsing/ selecting a new book. Better to keep the main library on computer, and just move books I'll likely need in the near future to the Nook.