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This is a late response to this post, but I think that maybe the problem is that node 9 is a constrained node in the diaphragm and then it is defined later as a retained node for the shear + moment transfer. Retained nodes cannot be used as constrained nodes in other constraint definitions. That is ...

The problem seems to be fixed adding -GJ $GJ to the fiber sections. In previous versions, for 3D problems, if GJ was not specified, the forceBeamColumn formulation would assume a big number (something like GJ = 10^10). You should be able to replicate the results from previous versions by adding -GJ ...