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Why the heck is my last comment flaged for moderation... okay I try it again. I found out there were commands like "G0 F6000..." in my gcode files and I found out that parameter came from "Travel Speed" in Cura which was set to 100mm/s... So I lowered it to 40mm/s for now and no more skipping occoring. Here is a quote from trinamic I just got
"The cause of layer shift is often too high start / stop speed. Reason: The motor driver must compensate for the back EMF of the motor during acceleration phases. The voltage-controlled stealthChop regulates the power more slowly, filtered through several motor steps, than does a current-controlled chopper like spreadCycle. Readjustment is only possible with continuous acceleration, not with jumps such as start / stop."

It would be interesting to know if people with the plugged TMC2208 module also have this speed issue...
For the VREF I've had values from ~0,94 to 1 or so, I set them all to 1,2V but that did not change anything to the skipping steps.
I will now try to increase travel speed and find out whats the max speed without skipping...