Minecraft 1.4.6, Minecraft 1.4.7, Snapshot 13w06a, Snapshot 13w07a, Snapshot 13w09a
Items in inventory do not stack consistently depending on if they were created before or after when you last logged out or did a Save and Quit.
Steps to reproduce:
1. Name a block of dirt "A" using the anvil.
2. Name another block of dirt "A" and see that it does stack with the first.
3. Save and Quit then open the world again.
4. Name a third block of dirt "A" and see that it does NOT stack with the first two.
5. Save and Quit then open the world yet again.
6. See that now all three blocks of dirt stack together correctly.