why it is different the out-put of transferfunction of SI and the model which is used with the same input in other simulation?

I select some Input and output and get the transfer function of the system via SI toolbox. I choose the model which is done by SI in other simulation. I select the same input of the system and use the Transfer Function it must be find the same output but I can not find it how I can solve the problem? I used the input and output in the SI then get the transfer function I want to use this model to check the output of the system but when ever I used the model with the same input it shows me different output any body can help me? tanx in advanced

[Yao Li]

Is the output totally different with or similar as the previous output?