I ran into this problem earlier today. It seems I had originally paired the controller in Nintendo switch mode by waking it up with [start]+[Y]. I had to re-pair the controller in D-mode by deleting the controller from recalbox, wait for it to go to sleep, put recalbox in pairing mode, then wake it up in D-input mode by pressing [start]+[B] and immediately press the pair button at the top of the controller