I would recommend doing this for only the first 4 load steps for one complete squarewave. Also, when you are applying acceleration in a positive direction the body will start accelerating in that direction, and even if the acceleration direction is reversed, it may continue some distance due to inertia, you can test this hypothesis by changing the time for the third step. Also, not sure why acceleration changes in z-direction in your model.
-Aniket
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