Skew Correction Issue

I got two parts that are the same. one is cnc machined and the other 3d printed. The 3d Printed one doesn't align with the cnc one. I suspect a skew issue I tried to set it up in RatOs, but it only improves a bit. Am i supposed to do it multiple times ? I did the Klipper method. If that helps. Or could it also be something else ike speed, acce settings or belt tension?