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.
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In that case, Tom, the problem is that it happens intermittently when dragging the stack around. Not only that, but it only works when I am dragging via right-click, which means I am only working with a half-stack to start with at best. Additionally, it does not divide all the items between all the slots.
I noticed this problem is only happening on my desktop, and not my laptop.
My desktop had an HD 6950 and a Core 2 Quad Q9550, and my laptop has an i7 and HD 5870 mobility.
This seems to be video driver related, for specific hardware setups.
Apparently my desktop is on 13.3 beta 2, which has apparently been reported by AMD as having OpenGL issues. I am going to install 13.3 beta 3 and see if it fixes the issue.
I believe #3 is expected behaviour and part of the inventory update.
Confirmed: See "Inventory Management" here http://www.minecraftwiki.net/wiki/Version_history#Improvements_.26_Changes_2