Does your Microsoft mouse use a different "control center" for your mouse settings? I know my Trackball does. However.. the settings in the mouse program will sometimes either stack or be bypassed by windows default mouse control (in Control Panel).
Double check your settings in both places and make sure the settings are pretty much the same value for things such as double click speed, scroll speed, etc.
You may also want to adjust your settings and then restart (not shutdown) your computer and see if that may help. Sometime helps to make sure your settings are getting recorded in the registry.