I've been having issues with the probe rack positions changing after shutting down and rehoming the machine. The rack shifts about 1-2mm from where it was calibrated. I've been looking for the tool.dat file but I can't find it. I'm running 2018 R2. I read that it can be an issue with the tool.dat file or the machine's home changes and will throw off the position every time the machine is homed.
For the changer, it's the toolc.dat (tool.dat is about artifacts)
The homing repeatability depends on the cmm, but 1 - 2 mm is much too large.
Maybe the probe was not calibrated when you performed the rack calibration ?
I used to run into this problem because we didn't have the proper permissions to write to the toolc.dat file, so everytime we restarted the demon it would revert back to an old rack alignment. Your IT department might have your permissions restricted.
I've put in a service request to IT. They used to restrict us from using the actual application and we were using a remote link but after asking for them to give us admin rights to certain folders we can now use the actual application. I think its an issue with admin rights.