I've had this issue with Oblivion, wherein the top left of the screen will show the windows mouse at the top left of the screen, and this screws up the mouse and if I click when it is over this small area it will go to desktop. This doesn't change at all whether or not my secondary monitor is hooked up. Of course, when I switch out of the game, no matter what workarounds are available on the internet, it simply will not come back up.
My setup is
Nvidia GTX 260 C216 65nm (drivers 270.61)
AMD Athlon II X2 240
http://www.ecs.com.tw/ECSWebSite/Product/Product_Detail.aspx?DetailID=892&CategoryID=1&MenuID=20&LanID=0
Windows 7 SP1 Ultimate 64 bit
1600x1200 monitor
Latest patch, I've installed the unofficial patch but it doesn't change anything relevant