Okay, I've pushed out a patch for this issue (It shouldn't require any configuration changes after you update the mod) but if you run into any other issues please let me know.
It looks like this was happening because when the Factorio devs made some of the new train logic in 2.0 (such as train groups or interrupts) they only wanted those schedules edited through the new LuaSchedule
instead of the legacy TrainSchedule
. I didn't test the mod with train groups, so I missed the corner case.
Thanks again for the bug report!