@ballboff I think that's kind of what he's getting at. We don't really know what customizations that particular build has, and how to revert them.
You may go to /opt/retropie/configs/all/retroarch.cfg and edit the main settings there, but do so carefully so that you don't break anything. The settings you may be looking for would have "overlay" in them, and probably there's one that says "enabled" which you do need to set to false.
If not there, there are different folders under /opt/retropie/configs/with the different emulator configs, but you'd probably be better off downloading a stock RetroPie image and start from there.