If you are using the same GPU to mine both SHA and scrypt at the same time then the performance will be cut in half from the GPU. It will use half it's resources for one mining and the other half to the other type. You wont be able to get max numbers mining both at the same time only when mining one at a time. A nice alternative would be mining BTC on some pools that also mine NMC, you're mining two coins at the same time with no performance hits.
But how come folding only has a small effect on speed?I'm not an expert on Folding@home, but I know mining uses stream processors. It's possible that folding uses a different part of your GPU to do it's work.
