What are you comparing? Time domain simulation responses ("model output" of GUI) or bode diagram ("frequency resp" of GUI)?
For time domain comparisons, make sure that you use the same initial conditions (x0). The on in the GUI estimates x0 such that the fit to estimation data is maximized. You can fetch the x0 values it used as an output argument of commands such as FINDSTATES, COMPARE or PREDICT. Use those values when simulating the model.