I get the gate to work by setting up the flight plan from the runway then, as the very last thing, zoom into the map and select the gate by clicking on the white dot i want on the map and then choosing “set as departure”. The drop downs don’t change but you can see the lines drawn on the world map.
When i go to the flight, the flight plan etc is correctly loaded and ATC recognises the flights plan too.
This is all post SU13