i play it in dos anyway. but the mouse problem is only there right at the beginning with the menu before the opening sequence. then it's fine. i really see no difference in playing it in windows or dos, so play it in dos (or dos prompt as i and probably many of you have) sound is a lot better and the mouse works like normal. or just go into the settings and control panel(don't worry, this shouldn't effect any of the system) from there double click on mouse and pointer options (may be different for those without win me, but i shouldn't think so) there should be a bar for changing the mouse speed. again, this won't effect your system, i don't know if this has any effect in the game (this is just a guess by the way) but it may help. change it back after playing the game.
this may help, or it may be a load of bull, but hey, it might help.