I assume you scrolled down through the misc tab looking for the stuff you sent there? If you hit up at the top of that list you should be able to loop around to the bottom and scroll up through any formulas to get to the books (should be faster than down through rocks and plants).
If not, save the game, then go through your inventory and send one weapon/armour/potion/etc to the battle tower (you can do this inside the battle tower), then check the chest again. Does everything show up?
