Thanks for the reply,
Yes i bought a new encoder, 1024 ppm was on stock. The label on the box stated 1024, but I will check on the encoder itself to make sure that is really 1024.
I thought because it has an index signal it was not possible to change the encoder PPR, it should give an error after 1 rev I thought.. but if you are right I could solve the problem by changing the PPR to correct the differences.. I will change the PPR to see any change in pitch.

I will check the Z axis calibration over a longer distance, I will let you know the outcome.
BTW when cutting metric M10 Ø10mm and pitch 1.5mm a normal nut will not fit, that is how I found out about the pitch error. A thread measuring gage does not fit either.
Thanks again and to be continued!