I have since learned that when rendezvousing with something it messes up. When moving to establish a new phasing orbit the blue node will move across the navball at the end (no idea about that) Then when making the next burn fro phasing it will have a timer of say 36 mins. The rocket will point at the node and burn immediately rather than waiting the 36 mins, the rocket will then go wild with the node moving all over the place and the ship being unable to rendezvous properly. Tried this on multiple save games with multiple ships.