$3 setting only reverses Y1 and not Y2

Hi, I built a CNC machine (Root 3 with lead screws) and I had it working with autosquaring and everything working fine. I decided to upgrade the leadscrews to M10 and in the process I mounted the Y motors on the opposite end. I reversed the setting in $3 for the y axis but it only reversed Y1 and not Y2. Is there something I missed or do I have to reverse the wires on Y2. Using the 8 bit Black box. Thanks

 

Thanks for your quick reply. Sure is easy with the screw terminals on the motor connectors