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(EDIT: If/when it does... it's a random bug sometimes).
At the moment, the only fix for when the game runs from the center of the screen (as in, the top right corner is in the middle of the monitor) is to switch in and out of full screen. Problem is, the new video options panel is too large. You've always needed to drag the menu off the top to click Yes, but the panel is so large now that to reach the yes button you move the Video Options button is off the top of the screen - meaning once it's in fullscreen, you can't switch back.