I have run into that problem more than once, LOL. What I did was enter the "STOP" command as the first entry in all the trains commands. This seemed to fix the problem.
What the F*** is happening to Trainz, I am getting very upset with this sort of stuff not getting fixed, along with a lot of other things. It seems no one is reading this form to see the displeasure that gamers are having.
If a route is up and running it will show here. You just need to click on the one you want to play. Also, you do not have to go here to start one. Just start the session that has the multiplayer rule in it.
Start TRAINZ game, click on "DRIVER / SURVEYOR" then at the top left click on "Type: ROUTES" go to bottom and click on "MULTIPLAYER". Hopefully you have all the assets needed but if you do not it will ask you to download them.
I had the same problem for some time and have not been able to find a solution yet either. I know it is a pain in the a** to move all the trains to their original location and I put a stop command in the driver set up menu of all trains, so they do not go too far.