There is a thread somewhere here in the forum which discusses this.
I think that the answer was that some flight just don't show the route even when its in the database. Also, there seems to be a bit of a "delay" in the routes showing after making a manual change. It might not show now, but it might show next time you run RB.
Also, remember that the Flight ID must match exactly - FCA556C will not show a route if it's in the database as FCA556.