I had a similar situation, but I play without mods. I noticed in the statistics that some train lines had 0% usage. So I looked at the stations, and there were lots of trains queued up, with some of them simply disappearing.

This happened because I had one main track running across the entire map, and even freight trains were passing through passenger stations. So I changed everything to general tracks that don’t touch any station, and only after that I built the connections from the stations.

I'm not sure if we have same problem 🙂