Could older settings be overriding the new settings somehow? When the game is run, where are the settings files created and stored? I can check to see if there's old settings files stuck somewhere causing the issue. Do you think maybe because I'm using a wireless xbox series x/s controller the setting isn't saving? That shouldn't happen though. I'm no dummy, been a PC gamer for over 20 years.
It's odd. I even tried running as admin with full screen optimizations disabled to see if that was causing it. Nothing I've tried works. The only setting that doesn't save is the invert y axis.