A machine tool builder like Compumachine had the ability to alter the way an axis references. Sometimes they would set up the machine to hit the physical limit switch, then reverse the axis and reference coming off the switch. Check the specific sequence used to reference the X and Y axis. That may give you a better idea of what's suppose to happen.
The message you refer to, "Z Axis Not Referenced," will be seen on the Status page as soon as the CNC boots and until you reference the axis. There will also be messages for X and Y as well. These messages will be there until the indicated axis is successfully referenced. You don't want to ask an axis to go to the Home position before it is referenced. Realize that the Home position is not necessarily the same as the Reference position for any axis - the verbiage DynaPath uses is different from other controls.
All that being said, you may have lost the marker channel on the Z axis. Can you swap the Z axis motor with X or Y to check?