My understanding of the operation of the drivers is that the direction pulse should overlap the step pulse at both ends, so whether direction is set one way or the other, High Low, 0v 5v whatever it should be in a settled state before the step pulse, then whether it is a positive going pulse or negative one, both the leading and trailing edges are within the direction state. I would imagine that if different protocols are used for step and direction then results would be unpredictable. As would happen when the timing of pulses is in error, then direction would not be properly set. - Hence missing steps.
JAZZ - correct me if I am being Naive