Do the double stacks appear while you are moving stuff around your inventory, or when you gain items? Anything specific about how you arranged the inventory and which stacks duplicated? I'm trying to get this to happen to me, but so far I couldn't. It would be easier to find the bug if I knew when exactly those extra stacks appear.
Well, I haven't gotten the bug in any of the newer versions of the game, but it happened when I moved stuff around. I moved items from inventory to inventory, but also around inside of the same one. I'd move everything around, close my inventory, get more, and then open it up and there would be duplicates.