I have been running 3 GPU's for a while without much trouble. I don't dedicate a core to the graphics card as folding@home is a secondary project. this may help keep the temps on the GPU down a bit.
AMDave
I couldn't confirm the ATI driver 6.4 works well with the GPU client. I was looking at this site link http://foldingforum.org/viewtopic.php?f=10&t=75 I don't have any of these GPU's in my main machine. I think I had your lag problem in the earlier ATI driver. I couldn't find any newer drivers for your windows 2000. Does the lag get better if you run other projects on both cores? Maybe this would free up the GPU enough to reduce your lag??
Good luck