Without looking directly at the model, it is difficult to know what is causing this behavior. I suspect the initial speed of the inertia you added ends up being non-zero at the start. The variable-ratio transmission has spring-dampers in it and so the input and output shaft speeds can be different. If the stiffness of those spring-dampers is not commensurate with the inertias, you can get behavior as you see on your second figure.
--Steve