I’m afraid I don’t know anything about the xcontroller, so I don’t know if it has any adjustments you can do, although I’m sure someone will be able to help you.
It looks like you are losing steps somewhere along the Z axis moving up and down. With the older style controller this could happen if your motors were getting too much or too little power.
I’m sure people have had similar issues due to the z axis vwheels being far too tight, or the two bolts holding the acme nut onto the spindle mount being too tight.
I think there was also someone that didn’t have the nut on top of their acme screw properly tightened which allowed it to move up slightly when it shouldn’t be able to