Conclusion jumping huh? I recall pretty clearly square stating many times that PAL roms will have issues. In fact it may even be just one page back.
And it's in the README. But I still try to answer people when they bring it up without saying something like 'RTFM', since I think that is a cheap shot.
Anyway, if you compile the trunk in the repository right now, I've inserted a Force NTSC option in the Settings menu - you can set this to TRUE prior before running a PAL ROM and it will try to run it at 60fps - this fixes the ghosting issue or whatever it is that is causing PAL ROMs to be this jerky.
However, it won't work on certain games because they had region protection (Super Mario All-Stars is where all the fun with 'region protection' began I think) and some games will even hang the emulator when you try to do this. It's certainly not the intended way to run PAL ROMs.
I read something in the SDK about ways to do a double Vsync in case the output signal is 50Hz while your main refresh rate is at 59.94Hz/60Hz. That might help, but slow things down when you're running NTSC ROMs.
In any case, I'd have to experiment with all of this stuff first.