It seems when using fullscreen, it pushes the image down, and cuts off part of the bottom.
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I'm using SVN build 461, I'm on Windows Vista X64 SP1, the latest DX9/10 SDK updates, the Open GL renderer, no filters. The graphics card is an nVidia GeForce 8500 GT with the 163.75 drivers. Does not happen when using the D3D renderer. The fullscreen resolution is 640x480.
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I cannot take a screenshot using the print screen key on the Open GL renderer while using fullscreen, otherwise I would post one. Instead, I'll put up a save state where the issue is easily reproducible. Just switch in and out of fullscreen to see it.