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Save robot in a given configuration not working

I am writing a model plugin to simulate a torque-controlled robot. I have a world file with the robot in the candle configuration. I would like to put the robot in another configuration and save it. I am able to move the robot correctly through pid control and save it. But when I load the previously saved world I have the joint axes not aligned correctly as it is possible to see in the figure below

C:\fakepath\Screenshot_2018-11-28_17-19-17.png

I have the same results by invoking setPosition() from the API. Is there any possible explanation for this? I am using gazebo 9.5.0.