Quoting Chancellor Maximus,
I had this a few times. I found that if you open your ship designer menu in game and then go back to the main map it stops.But in one case nothing worked so i saved game and re-loaded that sorted it.hope this helps.
Thanks for the help. I've also found that reloading saves works, but not always. I'll try switching between the ship designer and the map.
Does anyone know why this happens?