When you move Compare It! to the secondary monitor, the horizontal scroll breaks and scrolls vertically instead.
To be more specific, it breaks when you move the pointer into the secondary monitor.
i.e. Imagine you have your secondary monitor above your primary monitor.
Move Compare It! half way between the two monitors, such that the title bar is in the secondary monitor and the status bar is in the primary monitor.
If you scroll the mouse wheel in the bottom-left half the horizontal scroll works as expected, but as soon as you move the mouse to the top half, it scrolls vertically.
I've been using Compare It! for months now and just started using the beta version. It's great, solid software (except for this small inconvenience

P.S. This is in version 3.9.9.2009