Game Engine Problems

I'm working on my own game engine and I'm having a few problems with the speed. I noticed everything was pretty slow to begin with but just regarded it as bad programming or something. I have since noticed that my framerate jumps from ~50 to around ~8000+ when the app is minimized. Further investigation revealed that the CPU usage the program uses up jumps from 1% to 50% when it is minimized. I'm pretty sure this has something to do with the way windows manages multiprocessing but I'm not sure how to fix this. I'm thinking I need to learn a little about multithreading.

Any advice would be great..

Note: Torque works opposite of this, that is it slows down when out of focus, when in focus it uses ~50% CPU resources.