Oh my gosh this is an embarassing MESSUse CGMiner,
It will auto detect the best settings and auto adjust intensity dynamically for your card to ensure the best possible mh/s
However the Dynamic intensity is not as good as setting an intensity manually (wich yes you can do)
What is most likely happening is what the others are telling you, Your GPU, is reducing its clocks to a type of Power Saving mode because your "not using" the computer.
I dont use nVidia (because they suck) so i dont know how to disable its auto clock adjusting settings...
Stop touching your CPU, It's got frigging nothing to do with your bitcoin mining speed on a gpu unless your CPU is at >50% usage