@HopFrog I can confirm this problem.
If I drop the 2nd of the 2 item stacks, it takes from the first slot to drop items and then starting to drop from the last when the first is empty. If you empty the first one without picking up any new of that item, you will get it to stack in one slot again once the first is empty.
The 2nd slot is usually the one disappearing when inventory is full.
Otherwise a fun game! :)