Reasonable suggestion. I will dedicate some time tomorrow to extensively analyze and measure what 7K2 does and how it behaves when machine is on, off or with e-stop pressed. I should probably try to see if swapping the X and Z drives won't achieve something. Thank you again, I will post my findings.
Don't try swapping drives. At least on mine, the Z axis motor is larger for the extra force to fight gravity, so the drives, PID values etc are all different. I would doubt that there is a problem there. Sounds like a LinuxCNC configuration issue.