I believe I did what you suggested, I went to the retropie menu and update the script which took a while. I let it do its thing rebooted, and had to configure my controller to do anything. Was able to move around and try a test on the nes emulator, still same issue. I could jump and pause, and exit the game via hot keys. But that is all.
I did find a reddit post about hitting F1 and opening a menu and going to settings and I was able to config the joystick from there to work and save. exited and the configuration was still there. But only for that game. In the post it had a paragraph about writing down that configuration save name so I could post it to all NES games with in the emulator. Tried and tried through the command line $ to get it to work but got a error permission denied
at the command line I would type this
But get the denied permission, And I guess I really need to download WinSCP and try to figure that out