very odd – I’ll try and reproduce, but I have no idea currently why it might do that. I can only think that at the point of ES loading it doesn’t see the controller for whatever reason. If when it asks for controller configuration again, try pressing f4 to quit (and then a keyboard button to drop to terminal), then unplug and plug controller back in, wait some moments, and reload emulationstation (by typing emulationstation) – does it still ask ? is this consistent or not ?
Reply To: EmulatorStation is asking to reconfigure Gamepad at every startup