Let me try to say this in my words.
You want a train that stops, or returns to it's starting position, when the player jumps off. But why do you kill it then?
Here's my version (for stopping the train):
Every path ent for the train triggers a
trigger_relay that
would trigger the train off. For each path_corner there is a
trigger_once that is placed so that the player enters it just before the train reaches the path ent. This
trigger_once killtargets the according
trigger_relay.
To prevent the player from activating a
trigger_once while he is not on the train, use the train as the master for the
trigger_onces.
The train should also move faster than the player, so it gets switched off before the player could reach the next
trigger_once.
I hope this is understandable.
If you have further questions like this, please ask. I love those things.