Switching between monitors always caueses problems. I'm running 3 24" screen here off the one machine and bascially theres no easy way to switch between displays within 95% of games because as soon as you do the game will minimise.
Can either play the game in a window (which impacts performace) or learn to live with the fact that multi displays arn't meant for the vast majority of games, they only offer an advantage when running loads of applications within windows.
Also, if your display resolution on your monitors for a game is different than the the other display, the other display will lower itself, therefore mess up the window positions for apps you want to monitor on the 2nd display.
Its annoying, I'd love a driver/application that allowed you to press a button and allow you to interact with your other screens without minimising or impacting your 'main screen' where your gam is running, but there is none. The reason being is when you're in a game 99.9% of people use the mouse to look around..so if you where playing a FPS to look left it would automaticly move the mouse to the screen on the left therefore impacting the range of you looking left on the main(game) screen. Very annoying, but thats the way it is.