Ok so here is what I have going on.
I updated to retropie 3.0.
Im using raspberry pi 2 B+.

So one day, I got home and was going to play some super metroid. I noticed that for some reason, when I loaded it, all of a sudden the resolution had changed. I thought, “hmm that’s odd,” but no bid deal. I went over to sega genesis, loaded a rom, and everything looked fine. So I thought, “Hmm I wonder why snes would be this way but not genesis…” I went to NES, and everything was fine as well. So I went back into snes and hit my joypad button right after loading a rom to get into the launch settings. The video modes and everything seemed to be set where they should be.

However, when I tried to change the video modes, nothing would happen and it wouldnt save what I was changing. So I went back to sega genesis and nes, and now they were both doing the same thing. wrong resolution. It was as if retroarch could not find the config files for them or something.

I read that if you delete your retroarch.cfgs they will automatically regenerate with the default settings. So I renamed all the ones I had to back them up and deleted the one in /opt/retropie/configs/all and all the ones for my systems. When I did that, now when I try to load snes, it says “no config found for system snes”. It still does it even if I rename my original “Backupretroarch.cfg” that I renamed as a backup back to “retroarch.cfg”

So after having all this stuff go wrong, for whatever reason, when I load a sega genesis game, what happens with snes “no config found for system snes”, does not happen with sega genesis like I wouldve expected since I renamed my retroarch.cfg for sega just as I did for snes. But I notice that it is still the wrong video mode/resolution. When I hit the button to load the configuration right after I load the sega genesis rom the video mode is set at CEA-16 and retroarch is 1920×12…whatever it is. But that is clearly not what retroarch is loading when the rom starts…It doesn’t make sense.

I know this is a long list of stuff and it probably sounds confusing, but I described it the best way that I could.

The cores I’m using are lr-picodrive for genesis and lr-snex9x-next I believe im using lr-psx-rearmed for psx (It gives me the same troubles for psx) There just seems to be something fundamentally wrong with my retroarch and I can’t figure it out. Whatever other information you need that I haven’t posted, let me know.

Thanks for the help!