I observed that when playing PAL games in a LCD display set to a 50Hz refresh rate some artifacts arise. This is true when using a shader (observed in crt-royale and crt-aperture) in any core (tested genesis plus gx and bsnes-balances-mercury) specially on screen tilts (camera up-down motion). It looks like blinking or a shadow blink.
If I disable the shader it looks fine (well, some corner case artifacts with flashing lights like this one on alien soldier). I’m guessing but I wonder if the shader system is tied to the refresh rate or some aspect of the custom modeline in some form.