Hmm, well there is a known throttling issue with this board, but I'm not sure that would account for "significant slowdown". Have you tested the new RAM sticks, and have you made certain that the RAM timings are still correct in the BIOS?
It is to be expected that you will suffer a decrease in performance going from 6 GB to 12 GB which is why it's oft stated that don't get it unless you need it for memory eating programs. But exactly what are you calling significant ?
Look in BIOS at RAM settings ...they should match the speed and timings as advertised