I'm a total newbie to cnc and need some help or at  least a point in the right direction. I have a Zenbot 4848 with a Gecko 540 controller. My problem is that my Y axis and A axis slave are fighting each other trying to twist my gantry. If I unplug the A axis it operates fine. The A axis is operating in reverse. Did I miss something in the initial setup ?

In Config. / Ports & Pins / Motor Outputs - change the Dir Low Active state for your A axis then Apply the change.

Tweakie.

 Thanks. That did the trick.  Now my z axis is running in reverse of what it should be doing. Still running tests before I attempt my first cut. Any advice would be helpful. Thanks

 Got it ll figured out... It was the nut behind the keyboard... Forgot to toggle the reverse in the homing settings.