It might also be simply because you need to mess up with the screen placement of your monitor.
Don't ask me why, but sometimes monitors have different axis setting for different resolutions... And some monitors seems to be way off mark by default.
If it is the case, messing around the axis in full screen (usually 800x600 for old games instead of the now default minimum of 1024x768) won't affect your "normal" screen display.
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