A few things, don't set your minimul step size. (change it back to auto) Use the DAESSC solver. set both of your tolerance to 1e-3, 2 is far too large. Set your zero crossing algorithm to not be adaptive. Change number of consecutive minimum steps to 2. Move your electrical reference from the positive terminal of the machine to the negative (this shouldn't matter, as that dc-dc converter should be acting as if it's isolated, but just in case, it would be good to do). Also, your diode is preventing the battery from driving the motor (it's facing the wrong way)
If that doesn't help, share your model instead of screen shots, and watch this video: https://www.youtube.com/watch?v=QWTQqJ2Akmg&t=41s
