It is interesting that it was fine previously and is now stopping. We have heard reports of this a few times and suspect that it is firmware related since all Map Pilot does is load waypoints into the aircraft and off it goes. Map Pilot seems to expose the problem more than the DJI Go app does since it allows longer flights and gets used more. Also, DJI uses its own methods for loading the waypoints. We hope to have a new release that is based on a new SDK release in the next week or so. Hopefully it will address the issue.
Sorry for the issues.