Hi there Fredrik,
How are you driving the routes? If you're using Quick Drive that understandable as that's how it's set up. To get trains on a rotue you need to use an existing session or make your own by going to a route, clicking on Sessions and then clicking on Edit Session. You then place a few trains.
Then you save the session with its own name (for identification) and go back to the Sessions list for that route to drive it.
Kieran.