Is there the possibility that in modelling your structure you ended up with aliased superimposed vertical members in the model and only one set of these vertical members has the correct connection restraint to the top plate in the structure but both sets of vertical aliases are correctly restrained to the lower plates. If these is the case then one set of vertical aliases would only be displaced vertically by the loading of the lower plates and the top vertical displacement of that set of aliases would be equal only to the vertical displacement of the second plate from the top. The displacement display of the correctly restrained vertical set would also be masked by the exteneded ends of the other set.