This sounds like it could be a loose wire, or poor connection with the motor wires. Make sure all wires that are to be connected to each other are soldered and use a lineman's splice when putting the wires together. Also, make sure that the wires going into the driver is securely fastened.
If this is an issue where the motors have run well for a long time then just started to show this performance issue, then make sure that there are no wire ties or other binding method that is chaffing the wires. This would make the motors run oddly at certain travel positions where the chafing has caused a short with the wires.
If this is an issue where you don't have the motor plugged in at all and are just trying to turn it by hand and this phenomenon is occuring, then make sure all of the wires are not touching each other. When wires are touching each other and you are trying to spin the shaft by hand, the motor will feed current back into the motor making it difficult to turn.
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stepper motor runs smooth then rough for a moment then smooth, etc. Does this at all steps, and connected motors.