I'm no expert, but I guess such sync problems only happens if you use SCDConv. Try getting actual PAL versions, since those are re-programmed.
Unless a game is programmed to react differently to NTSC/PAL, it will have problems when converted with SCDConv.
A game that originally draws 60 frames at 60fps, takes 1 second to do it, will then draw the same 60 frames at 50fps, taking 1.2 second to do it.
It's like running emulators on slow computers: the game will play slower, since it has no "frameskipping" feature programmed. This is also aggravated by the fact most console games use frames as time unit, instead of seconds/milliseconds.
So they must be reprogrammed so they skip a few frames, or re-scale their speed variables.