From my understanding windows are not save in reference to the Top or bottom of the actual screen but from the relation to the letterbox frame. You can see this by adjusting the letterbox in game and watching your windows move up and down the screen. This is where the movement comes from as the game adjust the the letterbox from the resizing it moves the bag. I also notice in on hotbars also but not as pronounced.
disclaimer:
That was the behavior when I set up eXtreme's UISettings files. It has been a while since I've messed with detailed settings so things could of changed but I doubt it.
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