I had a problem like that on a river in my route. I solved it by adding invisible signals. I have a river that comes to a harbor area with a "single track" that loops back onto itself at the coal loading terminal, then at the other end of the river, the track goes into a portal that sends the boat back empty after a delay. The ships would turn out onto the loop fine, but when it came time to come back onto the "line", they would wait for clearance forever, even though it was the only ship on the track.
Use invisible signals on the "tracks", and there are switch levers that look like navigational buoys for a nice clean look.
