" throw their own signals." you mean throw their own switches? I'm using Navigate Via and Navigate To instead of the Drive commands, I forget why (alzheimers). I don't have "time out" as far as I know, altho I think I could use something like "wait for track clearance" to stop them from trying to pull out and pass the next train ahead. Or maybe I'm already using it, I forget (alzheimers again, at least I THINK it's alzheimers, I'm so senile I can't remember if I have alzheimers or not), I did have a problem where they would slide across to another track whenever a crossover was available, I think I traced that down to seeing a choice between a route with a yellow ahead and another route with a green further away. Or something.
This one;
http://www.youtube.com/watch?v=xJb_8UywoRA
I had to place two intermediate track markers to specify a Navigate Via for the most logical route - but without them, the AI DID throw its own switches, in a seemingly random pattern, until it hit a combination that eventually led to the next Navigate Via marker.
Some theories;
1. Markers after any facing point switch with an alternate path to keep the little culprits on the track you want them to take. Track Direction Markers usually work, but I HAVE seen the AI ignore them until it causes a traffic jam. Probably need to be added immediately after the junction so they won't even try to go in there.
2. Signals, signals, and more signals. AI traffic in MSTS was a pain when everything went right, when it went wrong the problem was usually not enough signals. Got 17 facing point and 11 trailing point switches between the AI train and the next signal, he's gonna stop at a red and spend a long long time figuring out how to set a path to the next signal. Not always necessary to have a signal before every switch, but it helps.
You might try this;
http://forums.auran.com/trainz/showthread.php?t=74640
And reverse engineer some of the things I did - altho be warned I still don't have a complete handle on this yet.