Best off-the-top of my head and first suggestion would be to retrace setting up your keyboard. You know the step that has you tell it what in's and out's its using? Try that step again.
But wait. How do you know its auto mapping if you cant hit a key and get any sound? When you assign a slider and move it or twist a knob while a device is selected, is it moving onscreen? Cuz then yeah, R6 is at least getting that data from your keyboard. So it is in fact communicating. Double check the in's and out's settings is my suggestion but its just an attempt to help. Odds of it being that surface are low. Hope ya sort it. Should be a pretty slam-dunk endeavor - ive got an Axiom 25 and an Axiom 49 and have had to sort things before myself.