I suspect that the acceleration/deceleration rate of the spindle is causing it, starving the generated leg, are you sure you have the controller on the right pair?
Another solution maybe to connect the main controller transformer (T1?) primary direct to the 240v 1ph mains supply, I show 2 10a fuses feeding it, if the drawing is the same as mine?
Set the primary tap accordingly first.
Al.
CNC, Mechatronics Integration and Custom Machine Design
“Logic will get you from A to B. Imagination will take you everywhere.”
Albert E.