Stuttering isn't the same as measurable changes in FPS...

First off, you should rule out any kind of overheating problems, as they are a common cause for all kinds of poor performance. Get a program such as CPUID Hardware Monitor, and see how high the temperatures of your CPU and GPU climb while gaming.

Also the brand and wattage of your power supply would be useful information, since those are not created equal and can also cause these problems.