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If you aren’t changing the grbl firmware, or setting the steps/mm with gcode commands, then it is making sense.
The arduino doesn’t know anything about the stepper driver configuration, so when you remove all the jumpers, it sends out one pulse, which rotates the stepper 1.8deg. So when you have no jumpers and you ask for a 1mm movement, it steps 4500 times (if this is what your steps/mm is set to in grbl), which is 2500 degrees. Way too much, and if it’s doing that very fast, then you will have problems of the physical hardware not being able to keep up. If you add some jumpers, then it takes 16 steps to move 1.8degrees, so it will only move 156 degrees in the same amount of time, which is at least physicall possible.
Whenever you change the jumpers, you also have to change the steps/mm in grbl, either by configuring and reflashing the arduino, or by using the gcode/$ commands to set them.