The setting is OS dependent. You set that in MacOS, it'll apply only in MacOS.
From what I remember, Windows doesn't have the appropriate setting, so you'll need to install a Synaptics (or similar) driver, to get full use of the features, like I had to do for the equivalent control over the ATi MBP graphics in both OSes.
In Windows checked through the Mouse options on the control panel. If you never use the mouse with windows maybe you can disable the driver or something...