It could be a faulty relay on the av bypass. Have you confirmed no issue exists with the rca leads? What happens if you turn av bypass off, do you get sound from left and right? (You will need to use both the marantz and sn3 volume controls with av bypass off).
I have tried 2 sets of rca cables, same results.
I have tried with bypass at off, playing with the controls of the sn3 and marrantz, same issue, plus the sound signal is perturbated.
I put my NAP150 back and all works with the marrantz.