I had a very similar performance drop when I last upgraded my system. It turned out to be the quad core! I replaced the quad core with my old dual core and my frame rates almost doubled.

I'm running Vista 64, 8Gb RAM, SLI nVidia 8800 GT, dual core CPU (forget the model).

When I had a quad core in this system I was getting around 15-25 FPS. After putting in a dual core I'm now sitting around 60+