I've got the same problem going on. What makes it worse is that the only way my game will run is in windowed mode, so when i open it up and the window isn't anywhere i can use it i cannot resize or move it.
The games that DO load 70% of the time i can't see all of the buttons, in the old version i never had this problem. just right click-minimize. I guess maybe it has something with the custom graphics being turned off as well and the custom resolution settings are inneffective too.
I'm running dual monitors and my main monitor is a wide screen. GeForce 6600 GPU