Carrier Landing single mission - landing waypoints not activating

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thing I immediately noticed is that it doesn't follow the route set out by the 5 waypoint roundels on the minimap, not precisely at least.

Second thing I noticed is that when the autopilot crosses waypoint 4 or 5 (it actually missed out one of the last 2 waypoints) it activates a series of other waypoints designed to bring you in for the landing and the tower gives him the all clear.