Gentlemen, -women,
Thank you for your help, I managed to resolve the situation. Indeed even though I had a batch of the same motors, with the same type no etc. there where internal wiring differences. For a few motors the pole pair wasn't on pin 1+2 or 3+4 but on 1+3 and 2+4. This was a learning moment for me seeing that in my experience using steppers I never had something like this happen to me. Perhaps these motors are a little bit too much 'china-y'.
What strikes me as weird though is that I have changed the motors on the board, testing the Z motors on the other steppers, which worked. So, not sure why.
Board is now working as intended, no more short-to-ground errors and sensorless homing seems to work a lot better on the X and Y axis now too.
Again thanks for the swift (correct) responses