I'm not sure if it has to do with the "Allow windows off screen or not", but I would suggest setting windows in their place in full screen, and hope for the best when going to windowed mode. I play in windowed mode a bit, but I run 1600x1200 and the screen extended as much as posssible. So, I don't seen a huge window shift, but there is a litte from the bottom, usually my 2 or 3 hotbars get shoved up a bit, and my chat windows.
But, one thing I know is that the settings can be different. IE: you can set a different resolution for windowed and fullscreen, so maybe there's different window placements? No idea.
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