I had the same when loading a simple pln, the route loaded into the world map and all the waypoints pointed to the north pole, I uninstalled Navigraph ( I had all the latest updates being a sub to navi ) after the pln loaded into the world map correctly, so a bug somewhere with Navigraph, very surprised as Navigraph being quite an expensive sub..
Hopefully someone from Navigraph can let us know why this is happening?.. thx