Never had this issue with TGO. (But I am starting to like TBC more than TGO now).
When importing a .job (or .dc) file into my project I get the "project coordinate systems are different" window. Those of you that use TBC know when you pull up the details for both, the differing items appear in yellow. The difference I'm getting is the Ellipsoid. The project Ellipsoid is GRS80 and the .job(.dc) file is Ellipsoid from Data Collector. I have both in my Coordinate System Manager.
The parameters for both are identical and I don't have any issues with horizontal or vertical so I'm not overly concerned about it, but I want a "clean" import.
Is the Ellipsoid from Data Collector based on the ephemeris that the receiver has collected for the day or is it something showing up in my Coordinate System Manager? Do I need to change a setting in CSD or in my controller?
If memory serves, the difference that is being shown is related to the name if the file, not the parameters of the ellipsoid (as you already noticed the parameters are identical between the data collector and TBC.
I never worried about it, but maybe naming the files identically on the data collector and TBC will give you a clean import?