Driving NEMA17 Stepper motor using leadshine driver
If the stepper position is out of sync with the driver they will often do this until the driver and rotor positions align. 

This is why normal practise to to 'home' the motor on system startup and then leave the driver enabled (so the rotor is held by the fields in the correct position), any time you need to take the driver off line you should probably redo the motor homing operation. 

Note that if your motor has limited travel in one direction, it is wise to run it a few dozen steps away from the home position before running it back onto the limit switch, this ensures that the thing is synchronised before it hits the limit. 

In this steppers are markedly inferior to proper servo drives, but are simpler to operate.