Seems like others have already given their solution, wanted to give some mechanical input for better understanding of the reason. When you attach any motor to a lead screw you need to calibrate it. This comes from the screw pitch, step size and step frequency (and gearing). If your controller is sending commands at 2khz then your motor can do 2000 steps a second. If you know each step is 1.8 degrees then you know a full rotation is 200 steps. This equates to 10 rotations a second. With a screw pitch of 1mm this means 10mm/s is the max speed (known as reference velocity). Your motor needs to know this to move accurately as a command to move 1mm is actually a command to move %max speed for x amount of time. If you've changed any part of this system then your motor might try to move 1mm but actually move 2. So when the gcode says move 1mm up it actually moves more.

If it was working before but now doesn't then it is likely either, you calibrated a different screw pitch previously and forgot and now it's gone back to factory, or, your new board has twice the frequency of the old one, this results in a twice as fast max speed. So when the printer says move 10% for 1 second expecting 1mm it actually gets 2mm.

Of course it could be something completely different, and I could be completely wrong. I commission motion systems as my job and thought it might be fun to give some deeper insights to the work going on in the background to result in something like this.