Does the pixhawk have to be connected to mission planner for you to fly in loiter mode?
I appear to be unable to arm my copter when there's a fast flashing green light. I get a amber light come on briefly. HOwever everytime I connect it to mission planer it has been switched to land mode despite the switch on the radio is in loiter mode.
If I switch between the mode whilest connected to mission planner it's works as expected.
I have made sure the failsafe for the station and battery are turned off then written them to the dataflash.
Any help will be greatly appreciated as this is confusing.
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Try apmplanner2 and post the .tlog it produces.
GCS failsafe is most likely to be the reason