Notice this: When you place an item X into a slot with item Y in the creative inventory, item X gets deleted.

This is even if the item IDs are the same, but with different damage values.

However... the same behaviour is not noticed with items containing NBT tags.

Note -> Enchantment Books.
They do not behave the same way as items normally would, because the only differing data is their NBT tags.

Simple fix.

Steps to reproduce actual bug, on 1.5.1:

1. Enter creative mode.
2. Go to the combat/tools tab.
3. Click on any enchantment book.
4. Place it down somewhere, and note the enchantment.
5. Grab that book, and place it back into the creative inventory, by clicking on another book with a different enchantment.

6. Place the book under your cursor somewhere, and note the enchantment.
7. Nothing happened to the book.

Expected Behaviour:
NBT Items should behave similarly to items with damage values as data, like potions and wool.
See working behaviour below.

Working Behaviour:
1. Take any item with damage values, like potions or wool or dye.
2. With the item under your cursor, click on another item, with the same ItemID but different damage values (another colour of wool, or another potion).

3. Note that the item under your cursor is deleted.

^^ This behaviour should be observed by NBT items as well, no reason why it shouldn't.