Likely cause of the error: The lecterns are programmed to drop the first available book after the first book is triggered during THAT game, but without repeats. If you replay, you never get the first triggering book so the game never advances the book count. I.E. it is a series of boolean switches rather than independent switches.
Oddly, Leah's books will respawn in any order, but I assume that is because they are event triggered and not chronology triggered.