I had the same issue when running Call of Duty 4, only the explanation was obvious. the default user access rights didn't allow the game to save the configuration thus every time I started the game it believe the computer's settings had changed and asked me to run the game with default settings, in this case 4:3 aspect ratio.
There where two ways to fix this;
1) run the effected program as administrator each time,
or
2)right click > Properties > Security > select appropriate user, or group of users, if not everyone > click edit > check full control.
I hope this solves your issue. It sounds to me like your driver and video card are doing exactly what they where intended to do, but the aplication is reverting back to a default state because you lack permission to save or modify application files.