One thing I have found that helps (prevent "short to vin" or "short to ground") is to raise the current of the offending axis slowly before sending any movements. So, for example, I have placed a 200 ms dwell/pause/wait after adjusting it to ~50%, then raising it to 80-100% with another pause after). Still not a explanation/solution, but it works better than anything else I've come up with.
