The exact same thing is happening to me except that I am only 2 boxing and using a dual monitor set up, no overlap between windows. But like he said when I am scrolling over to control my alt for whatever reason it seems that the "main" screen keeps wanting to "come to the front" and the mouse will reset on top of the "main" window, it doesn't seem to be just a mouse issue either, it seems to do this when I press keys on the keyboard as well(when I'm moused over the alt window). Sometimes after it resets it won't allow the mouse to scroll over the "alt" window at all and it takes a reboot of wow to fix. needless to say its pretty annoying.