it might also depend on the flavor of the linux, I don't know, which kernel the linux version is optimized for. Im pretty sure, that apesoccer's right in assuming that the benchmark is flawed in the linux-version, because the actual folding seems pretty adequate in comparison to the low benchmark-result.
My guess is, that the windows-version is better optimized. But its not a very educated guess. I could find out the exact specs of the linux-machine, I'm folding with, that would give us an idea of the relative speed, if we compare it to <A HREF="http://www.geocities.com/spitfire_x86/thgc/fahbench.html" target="_new">spitfire_x86's link to the benchmarks</A>!
cheers