Interesting piece of information here, that you may find helpful as a Troubleshooting Tip
All GCS900 systems post v12.7 use a CAL file for the Site Calibration, as do all versions of Earthworks. The older versions of GCS900 used a CFG file.
Trimble commented to me today that if you are having any issues with GPS Rovers not Matching the Machine Systems then you could try putting a CFG in the Machine vs the CAL file that is already there. There must be some subtle differences between the two options. I am checking to see whether or not this applies to just GCS900 or both GCS and Earthworks.