The rotary should have come with a straight and a cross-over patch cable. The cross-over would have the two inner wires switched,
Make your Yaxis cable match the Xaxis cable. Then fabricate a patch cable to correct the wiring. Another option it to cross-over the wires at the stepper motor end of the rotary cable (this is where you should have made the switch).
Another option is to purchase, or fabricate like mine, a Yaxis / Rotary switch.