Not sure whether it is a bug or a feature.
I have a railway track which consists mostly of bridges, i.e. one bridge next to each other without any non-bridge track in-between. When setting up a schedule, I have to specify intermediate waypoints as otherwise the trains can't find the route.
I have no such problems with r5828. Sometimes when building bridge after bridge, I forget to connect the two, but waypoints won't get by that.
Please provide a savegame for that.
Somehow it got fixed, no idea how.