In this game, lines 2, 25 and 26 require waypoint(s) between their destination to travel their entire route.
The route finding seems to be worse right up to or after a meandering river.
Shorter routes that also have both sea and river portions, like line 22 and 23 do not require waypoints to find routes.
https://dl.dropboxusercontent.com/u/17111233/test%2011.15.sve
Hmm - I know that ship route-finding is a difficult thing for the simulation to do, and I think that there are built-in limits to routing depth to prevent performance problems with this. A recent Standard update, which will be incorporated into the next major release (thanks to Bernd Gabriel's merging work) improves the route-finding ability of ships. I suspect that the best thing to do with this is to wait and see whether this resolved with the next major release, and, until then, use waypoints.