Im wondering if this is that 4k bug that is being resolved in 7.2?
Can you try your setup on a non 4k tv?
Im sure the config file though limits the resolution of the tv when running an emulator to 720p?
Do you have a Dreamcast or N64 game to try?
From memory they have lines in the config file lowering the resolution further to increase the frane rate, so they should display ok