Mach is counting the steps. It is delivering the steps. With different step modes, you have to adjust the motor tuning according to how many steps your motor will take for the desired increment. Inch/mm. When you change the step mode, the amount of steps it takes to move an inch also change. Mach is still delivering the steps you had originally tuned in. Your motor tuning is now what is out of time. Calculate and calibrate and it should work fine.