I'm having a similar problem with the naga blood. Basically I dropped it all in the well and after trying to drop in the 4th got a message something like 'the well is waiting for another item.' Apparently the game has a problem managing inventories, although the party leader (1st in the queue or designated char I don't know-just asked for that to be clarified) doesn't have the problem, and if that's what happened then whoever was carrying a book lost it-but since all items eventually respawn I guess I just have to wait. If you think this might be what happened and want to see more of it the thread is
here.
The other thing that you might have is that when you look at the quest it says something like 'all the evil book have been dropped in the fountain' and if that's the case it probably isn't the first time, just the first time you've noticed it. I've finished at least 2 quests that stayed in my quest list, and both times the quest description suggested that it was done. With at least one of them I had to tell Beriand I'd finished, since he was the one that gave me the job in the first place, before the quest moved into the completed list. Since he's the one that told you about the books maybe that's all you have to do.