This happened to me. I now know what happened to me: many of the story missions need to place custom tiles.
Which cannot happen on terrain that has been discovered.
So, they can only spawn in unexplored territory.
And they can only spawn a limited distance from the trade station.
This means that if you have been tootling around one area exploring, you will need to go to a faraway trade station to get the missions.
so, the fix is to go zoom to a far away or undiscovered trade station.
and then the missions should appear.