I think there might be different definitions for what a baseline is. I do not know what JAG3D expects as a baseline. What I have a for baselines is obtained from RTKLIB postprocessing of raw GNSS observations at the CORS and the new point. I understand these are east north and up components in meters. There is no use of any local or other coordinate system or geoids in obtaining these baselines.
These baselines are similar to what I get from other GNSS raw processing like Topcon Tools.
So maybe some conversion is needed to get the numbers as JAG3D expects them.