There are several possible reasons for the differences:
1) difference in the size of the columns with possible overlapping of the sections
2) Different number of monitoring points in the two models
3) rigidity of the rigid links (see penalty functions coefficients, you could increase their value)
Furthermore, you could achieve a better match if you subdivide the two columns in 4-5 sub-elements and connect all nodes along the height with rigid links.
Finally, note that strictly speaking this discussion is about structural modelling, and is a bit beyond the purpose of this forum, which is for the use of Seismosoft's programs. Maybe it would be better to discuss this modelling with your supervisor.
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T-sectioned Masonry Shear Wall Section Definiton
03-Analytical/modelling capabilities
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