A while back my Asus P5Q-SE gave out, and since I didn't have money for a same quality mobo at the time, I bought an Asus P5QL/EPU. I'm not too picky about performance, meaning I don't care if I keep a steady 60fps just as long as there is no noticeable slowdown. I didn't have any problems until I reinstalled Assassin's Creed II. From what I understand it's not a very good port, but I remember playing it without a problem with my old setup. I ran some benchmarks and found out that the framerate drops down to 25fps at times.
Since the only component that I've changed is my mobo I'm guessing that's where the problem lies. Do you think it's the motherboard? Is it the different chipset? Can it have such an impact on gaming? And if so, can you recommend a P45 board?