OK, looks like your almost home.
I'm assuming you have your fixed plate working, or you couldn't run the calibration.
When you run the calibration, you are also zeroing the Z axis, and the fixed plate location relative to Z zero is saved. And time you then run the basic Auto Zero, you are changing the Z zero location, which makes the fixed plate location no longer correct.
So, you basically only want to use the Auto Zero for a simple job with a single tool.
For a multiple tool job, you first run the Calibration, then the other tools will zero themselves.
Another option is to use the bottom of your part for Z zero. Then you calibrate to your spoilboard, and in theory you never have to zero or calibrate again, until you surface the spoilboard. That's why the calibration value is saved and restored when you close and restart UCCNC.
Hopefully, this explanation clears everything up??