I don't mean to be rude, but straight from Stanford:
-http://folding.stanford.edu/English/FAQ-Points#ntoc3
The reason GPU points are higher is because they do the math faster. They have hundreds of Shaders working together to allow for the math to be done at enormous speeds. The newer GPU Cores are likely more optimized than the older ones. (I don't know all the information about them, I can only assume based on what little data I happen to have.)
Thanks,
EBrown