I have a problem with these two games
The problem is: when I’m on the world map, I can’t see the minimap: I only see the red dot that indicates my position (actually, it’s more of a problem for FFVI than S3, because the minimap is useless there xD).
looks more like a bug in the emulator than anything that you can fix with settings. So everything you can do at the moment might be a bug report to the emulator you are using. The only option that I remember right now is, that on some snes emulators you can often disable some layers, maybe one of the is turned off. But by default everything should have been turned on, so I doubt that this is the problem.