I had a heavily enchanted diamond pickaxe (eff. IV, unbr. III, fort. II) and was trying to repair it on a heavily damaged anvil. I had two diamonds in two separate inventory slots. I shift clicked the pickaxe, which worked fine, then shift clicked each diamond separately. I hadn't got enough levels for the enchant, so shift clicked the diamonds back out of my inventory. The diamonds moved back to the original two positions, but now with two in each inventory slot. Upon clicking either stack the first would disappear, leaving just a single stack of two, which would not disappear when clocked.

Steps to reproduce
1. Put any tool/armor to repair in the 1st anvil slot.
2. Have seperate stacks of items of the base material to repair the tool/armor with.
3. Shift-click the first stack.
4. Shift-click the second stack. Notice after shift-clicking the item is still there.