It has been reported in the online game that the alternate directions feature does not work on the first pair of convoys on a route, both going in the same direction. The individual reporting it does not have a forum account (and has had some trouble setting one up), so I am posting this to remind myself to look into the issue when I have a chance and also as a record of the bug.
The steps to reproduce are given as follows:
(1) set up the stops and the depot;
(2) build a convoy in the latter;
(3) create a new line;
(4) set up the line and set the alternate directions;
(5) copy the convoy to make a total of two; and
(6) start both, both of which will go in the same direction.
I will look into this issue when time permits.
This has now been fixed on the 11.x branch - thank you to the person who reported it to me in the online game.