I've been having a similar issue to some of you. I've got a dual monitor setup (Windows 7 w/Aero), and run DCSW in fullscreen on one monitor only. I find that quite regularly Windows steals focus from DCS when moving the mouse, in some cases causing the sim to crash. Especially annoying when in the middle of a target zone and getting shot at while trying to adjust settings in the cockpit :)
Any help would be greatly appreciated as I'm really enjoying the hog otherwise. I've never noticed this issue in BS.