Not having had this problem the only thing I can think to check is, if you have some kind of software that came with your mouse try looking at the settings there, or if not try looking in Control Panel under the settings for your mouse, to see if there's some kind of "game mode" or "game detection" settings that can be adjusted.
I have those options in the software for my mouse and I seem to remember I had to tweak them a bit to make my overall settings for the mouse stay the same (speed, acceleration, etc.) when the software detected that I was in "game mode." But SH3 is really the only game I've been running on this machine so I don't know why it would be fine in one game and not another... but you never know.
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