I think there might be different definitions for what a baseline is.
Okay, that is possible. JAG3D does not expect baselines in WGS84. However, I expected the baselines in WGS84 because it is the reference frame of GNSS.
For further analysis, I used the transformation tool of JAG3D. The "source system" is defined by your provided baselines, i.e.,
CIQE 43433.6100 -45613.9500 235.4680
PUNT 87443.7240 -7622.0070 600.5070
RIDC 1551.9860 -1068.2310 15.8030
and the "target system" is given by the baseline components derived by the coordinates, i.e.,
CIQE -44040.196072607 4150.86462583952 44833.5778602501
PUNT -87256.470145868 -5971.42587897088 7402.66973277996
RIDC -1560.18983063602 37.8204587697983 1049.62383077014
I imported the coordinate to the transformation tool, i.e.
Since the original baselines as well as the derived baselines (from coordinates) are related to the new point CASA (i.e., there is no translation), the network rotations are unknown, i.e.,
Both system should be congruent to each other. The next figure depicts the results. The rotation parameters are given in radian (RAD) and are significant.
However, this is not the problem but the baseline components in source system (the original baselines) didn't match the components in target system (derived from coordinates), i.e.,
The last column (labeled by Outlier) indicates "gross errors" and ∇ indicates the assumed "gross error". All values are given in meters. As you can see, the values are very large. So, it is impossible to transform the original baselines to the values derived by coordinate components, i.e., both systems are not congruent to each other. Why?
Please note, this is my fist check of your data. If such checks failed, further analysis in JAG3D are not meaningful.