I had it in my game that at times it would run fast and at times it would run slower, mainly depending on the position of the pitch the ball is. It was annoying me but finally I fixed it. All I simply had to do was change it to 'Windowed' mode. It now works smoothly and goes at the correct speed throughout the match. If you are experiencing similar problems then give this a shot. PES3 is now 100% perfect for me!