Is there any configuration other than video mode on the pi4 that sets it apart from the pi 3?
I don't think so, but I don't have enough technical knowledge to guarantee it - I'm not a developer...
The difference I know is that Rpi4 has 2 video outputs, and that can influence: are you always testing with the 2 outputs to make sure that's not the problem?
The other option I know of would be to change the config.txt file, see if that helps:
https://forum.recalbox.com/topic/23950/7-2-mode-non-optimum/10