What can cause Z height loss in the first few layers?
Do you have any “slope” on the right side (non motor) of the gantry? I’ve noticed that my gantry will settle on the right side and lag behind the motor driven - ever so slightly - when it starts to drive up. It will, after that first lag, move fine for the rest of the time. Z axis travel seems barely affected but all my prints are consistently about .5 mm short.