All I can think of is that it must be your screen scaling. For example, if you have an NVidea card and a screen running at a high resolution, you need to "tell" the card through the NVidea Control Panel to use NVidea scaling when you're running a program with a resolution lower than your system's native one. SH3 runs lower than 1600 x 1200. So to get full screen display you have to adjust your system to give you full screen by scaling. If you use scaling with fixed aspect ratio, or don't scale you'll get the partial display.
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