After a long time of trouble shooting I found the issue: Only the trains which I did not place on the rails by hand were affected. Both the control station and the trains needed to be placed by hand. (For automated construction I use the repair turret mod. That mod and this one seem incompatible.)
This sounds like a proper bug. Looking at the code for the main repair turret mods (the original by klonan and the repair turrets 2 fork) it should all work fine.
Can you please specify the exact mod for me? I did try to do some testing but I don't understand how to make the repair turrets build things. Could you explain how to trigger that so I can test it?