This could be fixed in the latest version. I couldn't reproduce it.
Are you using other mods? Anything you did to the train after entering it (switch between auto/manual mode, dis-/connect wagons, pickup/build a wagon)?
Yes, i am using many mods.
No, i'm just leaving the train, window with trains close up and then i have to re-open window.
Thx for this mod, it's wonderful