This has been discussed in a few other threads before. You might find various problems as you change settings..this is my experience:
v-sync off, frame skipping off - game runs smooth and correct speed, but with screen tearing..
v-sync on, frame skipping off - no screen tearing, but cut-scenes, corners, free kicks etc. are far too fast (unplayable)
v-sync on, frame skipping on - no screen tearing, but everything is much faster than it should be..
Unlike every other PC game I have EVER played, for some bewildering reason Konami seem to have bound the game speed to the monitor refresh rate. I needed a 60hz refresh rate.
If in another application you have forced the refresh rate of your monitor higher than 60hz, PES2009 seems to run too fast or badly.
Please try Frame Skipping on, Vsync on, 60HZ.
Hope this helps.