Perhaps it might be the mothboard or a "dying" cpu. Have you tried overclocking the i7? Do you have proper cooling for ocing? If not then I cannot recommend anything else because I have never seen this issue before... It might just be the files your copying or how your copying them...I really don't know... :\
File transfer speed has almost nothing to do with your processor, it is hard drive limited usually. What are the exact models of your hard drives? My guess is the one in your Q6600 system is actually faster. It is also possibly a difference in OS since you didn't give us that information, or a difference in usb performance between motherboards.