@MinivanDriver i noticed a ; too many in front of the name [USB Gamepad] in the /opt/retropie/configs/n64/InputAutoCfg.ini file
Example:
; InputAutoCfg.ini for Mupen64Plus SDL Input plugin
; USB gamepad_START
[USB gamepad]
[SWITCH CO.,LTD. Controller (Dinput)]
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = 4096,4096
AnalogPeak = 32768,32768
Mempak switch =
Rumblepak switch =
R Trig = button(5)
Etc.
Remove it, and try it. I think it prevents the .ini to start the pad configuration