G0 not zero? (more info)

Not sure this is the correct topic, or where to start figuring out this problem.

I have a new build LCNC 2.9 from disto, EtherCAT, AC Servos with/ 23-bit absolute encoders, using ProbeBasic I have attached a screenshot with the issue show the Z-axis

"Sometimes" the "zero" will not display as zero, most of the time it works and will display as zero.  On the screen, it will show a non-zero value (-0.297), and a G0Z0 does not move.  If I move off that value and G0Z0 MDI, it moves back to the same non-value, also "zeroing" the Z-axis does not set the value to zero.  I have seen this on all the axes, not just the Z, but the same issue.  I have not seen a pattern yet, or what triggers it.

I am looking for an idea to explore the issue further.
Thanks!!!!!
 

After further testing and focusing on the Z axis, it is related to the limit switch. If I Z+ to the limit, then re-zero the non-zero value increase (G54). Each time I bump up to the limit switch, the value increases. Strangely, the actual (G53) remains the same (within a few tenths)

Also, if I "power off", meaning use the power button of the UI, and then power the system again, I can then correctly zero the Z. Meaning if I then press the zero Z axis, it will then set to 0.

BTW, thanks for helping!

I have limit switches on the Z-Axis, lower and upper. I

1. Jog positive and trigger the upper limit switch
2. Jog negative off the limit
3. "Zero" via the UI the Z-Axis
4. The W54 Z-position will "reset" to a non-zero number
5. The absolute machine position does not change
6. repeat 1-4
7. The "zeroed" W54 position will increase by around .300 with each jog cycle.
8. The absolute position remains the same for the Z-position I am zeroing.