Well , My enchanted books did not glitch out in an ender chest for several days , It's for sure a bukkit problem but I don't think you can avoid this annoying glitch then.
Quote from Minecraftwiki : "Sometimes enchanted books lose their enchantments. When you hover your mouse over it, the name will simply be "Enchanted Book" and will not show enchantment. They will not work if you try to apply it to a tool."
