The multi-track switch bug was constantly reported as a problem on this forum, but never fixed by CO. You have to, either add a single track loop, or downgrade the multi-track to double track as a workaround for the problem. It's really annoying!
The multi-track lines are of very limited practical use in the game due to the inability of placing stations on their inner tracks. It's a feature of the game that was never properly developed and would have had the possibility of a major upgrade had CO been interested in further developing the game.