Hi, Danny
Set your Active Low setting to the same "State" as your Z,X in Ports & Pins, Motor Outputs page, See if that fixes it.
If there all the same (As thay should be), Then you may have a bad connection on the Y Dir Pin.
If your axis runs backwards, Use Home & Limits page "Reversed" box to change the Direction (This is the proper way to change it).
Hope this Helps, Chip