This bug has been in a game for a while and in Minecraft 1.4.2 it is still not fixed.
It actually happens if you play on the server, not sure about single player version.

Description:
If you click a chest with right mouse button several times before the chest interface appears, then all interaction that you will make with items in the chest will be undone after you close the chest interface. But you will not realise that until you once again open any chest (or Furnace or Dispencer or Ender Chest or Crafting Table). Opening of inventory does not update information about it.

This video demonstrates the bug: http://www.youtube.com/watch?v=OS1uEU35YyQ

Steps to reproduce the bug:
1. Open a server with ping over 150 ms
2. Place a chest, get some items to your inventory
3. Click a chest with right mouse button at least twice before it opens
4. Make some of these interactions:
4.1. Move some items from your inventory into the chest
4.2. Move some items from the chest to your inventory
4.3. Change the order of the items in the chest or in oyur inventory
5. Then close the chest
6. Now if you open your inventory, you'll actually see fake items because interactions with chest you just made on the client side were did not really happen on the server side
7. Open a chest again to see the information about inventory updating on a client side

The same thing happens with ender chest, but does not happen with dispencers or furnaces.
So I imagine it happens because of the animation of opening/closing the chest.

Double rightclicking on the chest also breaks the animation of opening/closing the chest: the chest remains opened even when you quit the chest interface.
I guess, this happens because the system thinks that after you first entered the chest interface, you did not exit it and still looking to it.