Hi Agmut!
Firstly, could you confirm for me that you have train loading enabled in the mod settings (per-map settings)? This is disabled by default for balance reasons, and also because it disrupts a lot of popular train station blueprints.
If it is enabled, then this is more than likely an error on my part in the train loading logic. I'll look into it, but it would help me diagnose the issue much more quickly if you could link me a copy of your savegame on google drive, etc. I'm working on the 1.1 update for the mod right now, so I'll see if I can reproduce the issue while I'm at it. I'll let you know here if I'm able to find a fix.
In the meantime, let me know if you have any other problems, and thanks for using the mod!