Currently, when you have the ship menu open and you click on a blank piece of ‘map’ in order to scroll (not on a ship or star), the menu closes. I think it would be better if the menu would remain open, just as it happens with the Empire menu, for example.
After creating some waypoints, you’re (I’m) usually trying to assign different orders for each waypoint. But when trying scroll the map in order to center on a new waypoint, the whole menu closes
Another thing that might help in this same situation is having the waypoint destinations clickable, in the menu (i.e. if I click on a star name in the waypoint list, the map pans to that star, like it currently happens when a star is linked in a Diplomacy message).
While both solutions help, I think the first one might be the easiest to implement, and definitely the one that would decrease UI frustration the most.