My config must be screwed, I'm going nuts?

Still a bit fresh in the world of retroarch, but have been working on vertical overlays.

Anyway was just checking some ROMs after a manual content scan. And when testing one that was using the wrong mamecore, things started to go wrong or maybe before then, but can’t remember now. Things like Retroarch started in windowed mode, overlay of game was showing and every time I think I fixed it it comes back or something else gets screwed. Like my shader presets are now off. I am going nuts chasing around. Is my config file saving correctly.

I don’t know enough about the system yet to know which files to look at or what is going on. Already find the saving of configsca bit confusing to begin with, so maybe that is my problem.

Anyway help??

Your retroarch.cfg is where your global settings live. Your overrides live in RetroArch/config/[corename]. If you delete your retroarch.cfg and everything in the config dir, it should be pretty close to a fresh install