Vehicle Stops executing Mission

I am using a companion computer to load missions to Copter and since upgrading to 3.5.2, I’ve observed some interesting behavior where occasionally after uploading a new mission it stops executing the mission after the first two mission commands (an ROI and a waypoint). The vehicle stops and waits but will resume if it is sent a mission start command.

When uploading a mission, after I get the mission_ack signifying the upload is complete I send a mission_set_current mavlink message to set the next command to 1 (thus starting the new mission). It seems to occur randomly–but this is what I’ve observed:
– I always get the mission ack with MAV_MISSION_ACCEPTED
– I always get the STATUSTEXT message saying flight plan is received
– I always get a MISSION_CURRENT message for mission item 1 (which is an ROI) and one for mission item 2 (which is a waypoint)
–the mission will resume executing if the vehicle is sent a mission start command from mission planner.
–this always seems to occur after hitting the first waypoint
–the behavior occurs both during flight and in the SITL simulator
–the mission it occurs on seems to be random.

Does anyone have an idea of why this would occur or where I could look to troubleshoot it?