When enchanting an item that you have two of in your inventory (i.e. two swords, two books, etc.) the enchantment does not always apply to the item added to the enchanting table. For example: with 2 normal items and I enchant one of those items it'll get the enchantment; but then enchanting the 2nd item only gives the first enchanted item the enchantments that the 2nd item should have received.