what is the problem with system id toolbox?

Hi I use system identification toolbox in frequency domain and the pss method. After I get the identified system I use the method "by initial model" and give the toolbox this obtained model to reach a better identification. And after i see the identified system is acceptable, I export it into workspace. the problem occurs when i use "ss" to reconstruct the identified model which is not the same as the one shown in the toolbox. I mean the bode diagram obtained from workspace is not the same as the one obtained in toolbox using "model output". why?

[Rajiv Singh]

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.