Yeah, without knowing the exact application and the model, it'll be hard to speculate... but i'll try anyway:
In any finite element model, you have to be cognizant of your boundary conditions, restraints, and your element definitions (plate, shell, membrane... etc). If you're modeling a shell element, you could have axial forces imposing compression or tension that in places that you're not considering. Plus, if you're doing a time history analysis, to which you refer, the results will be dependent on the dynamic modal behavior of your modeled structure.
In short, paying special attention to your element definitions and boundary conditions will help you better understand the model.
I suspect you may have pinned joints that would behave differently than if they were rollers, for example.
Also, in SAP, you can specify which degrees of freedom to consider in design... which can offset some of the uncertainty in boundary restraint (try only analyzing Uz if you're only interested in vertical displacements, and don't want to include axial deformations which would influence the vertical displacements)
Sorry if it's not much help... but Good Luck!