Issues with Block by Block analytic Linearization algorithm

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Hello,
I'm having a unexpected issue trying to linearize my Tandem Helicopter non-linear simulink model. I'm using the L.A.T (Linear Analysis Tool), but I have the same issue with linmod. The trimming processed is done using the L.A.T.
Here is the issue, the algorithm apparently modifies one of the model's sub-systems parameter input (a normally static 1 or 0) which triggers a error. I also tried specifying the linear analysis points explicitly.
I tried using the numerical perturbation algorithm but the resulting state-space is incorrect.
I would greatly appreciate any help.
Thanks

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