I think I just found the reason for the massive step skipping. As you sugested I decreased print speed and accelleration in cura below 30mm/s, but I still got step skipping. Wondering why this happens I opened the gcode and looked through it and I found "G0 F6000 ..." commands, that is of cause HIGHSPEED :D. I missed the travel speed setting in cura, it was somehow hidden and set to 100mm/s. It seems those drivers are really speed sensitive. So I just set "travel speed" to 40mm/s and oh wonder... no skipping anymore. Would be interesting what's the actual number limit without skipping steps.
Here's another explanation by "Bernhard" from the Trinamic Support:
"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."
For VREF I've found values from 0,94 to 1,03 or so, I currently have all set to 1,2V, but that did not change the skipping.
I will try to find the optimal speed settings step by step and live with that, as I said next week I will maybe take a thermal look onto the board and then I will see how the resistors are doing :)