I know that with new chapter updates in order to get more accurate protein energy scores it has put a higher load on the cpu. not just with calculating the bonds and everything that goes into the score, but with rendering the protein as well(like any bonds it may have, voids, exposeds, bands, cut points) If you simply deferred the calculations from the cpu to gpu on just rendering, the overall performance of foldit should increase.

I don't know everything, but using the cpu to render this is a waste of processing power in the grand scheme of things.

http://www.youtube.com/watch?v=-P28LKWTzrI

That effectively shows the difference in rendering images of a cpu and gpu. Ignoring a resource that is better for certain tasks is foolish and in the end more time consuming.