Windows has this irritating behaviour: rolling the mouse wheel scrolls the window that is in focus, and not the window that is under the mouse cursor. This can be fixed easily by using KatMouse, which enables the latter behaviour without changing the original window focus.
By default, KatMouse assigns the scroll button press to some other functionality. This is also irritating because I use the scroll button press to close tabs in browsers and other software. So, it might be a good idea to turn off this feature. To do that, open the KatMouse properties by right-clicking its icon in the system tray. Go to Wheel Button and choose None of the buttons as push button.
Tried with: KatMouse 1.04 and Windows 7 x64