You guys are right, the windows are stored relative to their positioning in the main window so that when the window resizes, the windows move with it. It makes sense because if you have hotbars, chat windows, etc at the bottom of your screen and you drag the window bigger you wouldn't want those windows floating in the middle now.
We could possibly add a new value for a window that says ignore those alignment settings. I also seem to remember code that takes the letterbox into consideration when aligning the windows, but it might have been based on an option that you can toggle on or off.
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