Cannot save retroarch settings

After reinstalling from Pixie to Loose Goose, I am not able to change retroarch settings. I’m clicking ‘Save current configuration’ and it says it’s saved, but when I quit retroarch the settings are reset. I’m just trying to change Theme settings of retroarch menu and set up retroachievements

Furthermore, retroarch looks different now: instead of minimalistic pixelated text it has more of a ‘default’ look now

edit: when I save configuration from game-specific retroarch menu, it says ‘Not saving. Override active’

This is all covered in the following FAQ.