I'm facing the same problem, but with a small diference. I'm running the simulink from GUI, but when the simulation finish doesn't apear a variable 'simout' in my base workspace. So i can´t plot the result on axes. I'm using a variable block in simulink, to get all the data to worspace. The only way that i found to get a variable in base workspace, is to run the simulation manualy in simulink.
what can i do to solve this situation?
Thank you very much.