System Identification Transfer Function response is different in simulink

I used system identification toolbox to generate a transfer function from measured step response data. Note that the measured data is non-uniformally sampled. The compare function shows 95.3% fitting.

I then referenced the transfer function to a LTI block in simulink.

The response from the transfer function output of the simulink block is different than the output of the compare function.

Why? What am I doing wrong?

* See code snippet below *

measured data is cm_mat_trim

[cm_mat_trim_re(:,2), cm_mat_trim_re(:,1)] = resample(cm_mat_trim(:,2), cm_mat_trim(:,1), 4);
test = iddata(cm_mat_trim_re(:,2),cm_mat_trim_re(:,3), 0.25);
sysTF = tfest(test, 2, 0, nan)

figure(4); compare(sysTF, test)
figure(3); plot(CtrlOut.time, CtrlOut.signals(2).values, 'b', cm_mat_trim(:,1),     cm_mat_trim(:,2),'g') %compare simulink transfer function output with measured data

[Geo]

Hello Vincent,

I just have a similar problem where the response shown in system identification toolbox is different than the response simulink is giving me. Do you happen to remember how (and if) you solved it? Thank you in advance.