Do you mean that JAG3D expects baselines as differences in the ECEF system? I think the topography software is giving baselines in a NED o ENU system https://en.wikipedia.org/wiki/Local_tangent_plane_coordinates
Did you consider this in your previous conversions?

I still do not understand if the problem is mismatched concepts between software, a software bug, or bad data. I can produce new data to other goverment CORS or to private poins using a pair of GNSS receptors.

Thanks