Hmm
I'm not sure if this will solve the issue or not, but lets try anyways:
Go to Start> Control Panel> (to the left menu, click Display All)> then find Mouse
Click the Wheel tab. Try lowing the number of lines skipped per scroll to 3. If the problem continues (or if its already set to 3) then it may be a problem with your mouse software. If this is the case, then you should update the driver.
What sort of mouse is this? USB or PS/2 (standard)?
What brand of mouse is it?
Do you know of any special software designed for it?