I don't mind at all helpman
I did notice your issue myself on the very first page of the setup wizard after choosing Advanced. I wanted joystick input and I didn't want anything executing shutdown my PC.
This happened two or three times and right when I was going to report it, it didn't happen anymore. Everything I change is saved now. I don't know if it has to do with executing the verify and the end of the wizard or if it's just dumb luck.