Hi,
my guess is that the Step/Dir outputs of the controller are not strong enough to drive both driver inputs.
The driver inputs are photodiodes, and diodes of any description including photodiodes are inclined to 'current hog', where one photodiode conducts
all the current when the second photodiode is yet to reach the voltage threshold for conduction.
Try a dual channel opamp between the Step/Dir output of the controller and the two driver inputs. The two inputs in parallel will not work reliably.
Craig