Thanks gentlemen, it was a missed track connection, there were 2 splines almost on top of each other which were not connected that I had missed.
I had also forgotten about the message window for clues, thanks for that reminder.
The save game method in Trainz has been abit confusing and has led to some real head scratching and restarting routes a few times due to missing items from unmerged sessions. Last time Trainz created a session with having no option but to say ok, I used a swear to name the session (got a little heated over the last route which had 20 hrs or so which suddenly was all messed up) since then it seems like I kinda got the routes and sessions saves figured, but now I got a real nasty session name which keeps getting overwritten, hope I can change that.