In my experience, if I've just booted my computer up and turned my control power on, I can count on having to 'zero' my axes, because I have no idea how they've moved while it was down. For some machines, that means using homing limit switches. I don't have those installed, so I home manually (the way a machinist with a DRO does). But in any case, having just jogged the axis before zeroing, the step control is now properly somewhere in the middle of its phase sequence, holding steady and waiting for the next step that you command.
Also, when you energize one phase of the motor, the rotor
will snap to that position, no matter what position it was in before. It may jump across those 2 or 3 magnetic 'detents' to get there, but I assure you, it will get there! That always happens on my control when I first turn it on. It goes to 'phase 1' from whatever phase it was on before. And as long as I accept the fact that I have to zero the axis then, I'm OK with that.
Brian