I've been playing from the start and I don't remember this issue arising until after 1.4x.
Basically at a new turn you get the blue icon that says your new ship is complete. Click the blue icon which brings you to that planet. Double click the new ship to launch. Then you click the destination you want that ship to go to (at this point there is a blue ring around the ship and the planet info is still listed in the lower middle pane.
What happens, however, is that a ship that was hanging out needing orders elsewhere is moved.
It used to be that when a ship required orders it would be auto-selected and it's information would appear in the pane below to let you know what ship you were dealing with. I think it auto centered on it too.
Obviously, this is not happening for me now. Is this a bug or not?