Sounds to me that:

You are using this computer at same time as mining .
Cgminer is setting to  dynamic (Default) only uses one thread.

Try this...set cgminer to an intensity of 2 . It will then use 2 threads @ an intensity of 2. Now ramp up the intensity till your temp and or responsivness is what you want.. I can use a computer at intensity 7 and the temp will l remain at a reasonable level. (9 gets a bit sluggish).

Open your cgminer.config have a look around. Read the readme (its actually written very well ).

Set Cgminer to "Auto Fan" "Auto Gpu " With a temp of say 70 c. (this is what I use).

Set it and Forget it.