I'll be interested in that map zombie
Personally, when I try to make AI move in a train, they go along fine.
Are you making the train start of at an Upwards hill? This will cause the train to go backwards at first, then go very slowly, stopping every now and again.
Also, have you got another train on the same track? A problem I had when I had 2 trains is they would move, then stop, then move, then stop etc.