Summary: When /replaceitem entity <player> slot.inventory <n> <item> <count> is running in a repeating command block, items are not removed, moved, or thrown correctly

Steps to reproduce:
Fixed (1.2.5)

1. Place a repeating command block (powered) with a command such as: /replaceitem entity @p slot.inventory 20 emerald 32
2. Pick up another item (such as 2 diamonds)
3. Select the 2 diamonds from your inventory onto your hotbar
4. Attempt to throw the item or put the item into a container

The items should now be on the ground / in the container, AND still in your inventory

1.2.5 Issues
As of 1.2.5, this affects the hotbar in strange ways. This will cause you to sometimes be unable to select certain objects in your hotbar and, even when it seems that you selected the object, it doesn't actually do that.