You should not be losing a step in any of these processes. I can say that if you change the pen height, that can result in a misalignment. Try to ensure that when the pen touches, (1) it is pointing directly towards the center of the egg axis and (2) the distal pen arm is as close to horizontal as possible. That will minimize the effect.
You could also be having an effect of the egg “wobbling” in the egg couplers, so that it is not coming back to the same place after a full rotation. Try to wiggle the egg when it’s in the couplers: Does it feel solid and secure in place? If not, you’ll most likely have this kind of issue.
