There seems to be an issue with Java input where if you click, Minecraft will continue the click operation for a short period (between 50-250ms)
For example, if you right click to place an item, it will function as if you have held down the right click for 200ms, so in the case of Minecrafts' new inventory management, it will fill any empty squares you pass over with an item from the stack you are holding.
There might need to be some optimization so input latency can return to pre-1.5 status. Players should be able to manipulate inventory as fast as they can click.
Seems to be related to https://mojang.atlassian.net/browse/MC-12598
I updated jinput.jar to the latest version and it has appeared to cut down the lag to about 50-100ms, but the issue is still very prevalent, indicating something that has changed in Minecrafts' code, and very likely due to the new changes to inventory management.