I assume you are using ISBoxer Window swapping? I've had that exact same problem, and from what I can tell, it's a performance penalty caused by the GPU rendering information but displaying it on a display powered by another GPU, such as the onboard.

The best way to do it is to not cross GPUs, meaning your main screen is on the same GPU as all of the slave windows.

I ended up upgrading to a 6 core CPU and it did wonders to my performance. One thing that helped my performance, was to have no wow clients using CPU 0, leaving windows, and internet windows their own CPU.

Also you could try overclocking.