The D1x uses a linear potentiometer to provide precise location information for each shift point. The linear potentiometer is prone to wear and damage especially if dirt or water enters the drive tunnel. In that case, the potentiometer can be scratched leading to an erratic movement of the motor at certain shift points.
If that happens, attempt a New Configuration but begin the smallest gear at a position different from the previous configuration. That may allow you to "jump" the errant location on the potentiometer. For example if your first three gears were at 100, 160, and 220 and you noticed erratic behavior at 220 you could start your first gear at 130 then the next two would be at 190 and 250 which would mean that the motor never tries to locat at 220 thus extending the life of the potentiometer.
Another cause for erratic behavior could be that Settings > Overshoot is turned on and misconfigured. Attempt to turn that off and/or change the settings to different values.