It's true that many (if not all) cores output slightly out of TV standard freqs. Real PAL resolution is 312.5lines per field. I don't remember any core providing exactly 312.5lines(may be only Minimig - but i didn't check its code as it's too complicated). So if core provides only 312lines or even 320lines - the vertical frequency is already doesn't match to standard PAL. So, you will have stutter issue if you will output to PAL. I suggest to set scaler output to 60Hz(NTSC). Stutter will be less noticeable.
I will give that a shot. Thanks for the info.