linux should do absolutely nothing to windows on a separate patition. this is assuming of course that you haven't mounted that partition and gone mucking around...
could it be that the mouse is the problem, and not the driver, or linux, or some such software problem?
i'd do the usual...check that the connection between mouse and comp is good and snug, make sure that (if it's a mechanical mouse (non optical)) the inside wheels are not covered in crud. (take out the ball and look at the little rollers) and if it is an optical mouse, make sure that nothing is blocking it (hair, schmutz, etc).
hope this helps.