Came across this issue again when on the 13th (coincidence?) chapter where you reverse round the loop with the ACS-64. When approaching the signal just after the crossing on the the loop it was red. I checked the map and it appeared that an AI train was in the way. After about 10 mins the AI train still hadn't moved and was starting to block other services. Thankfully after quitting the service then trying it again it worked fine.
Ran into a similar issue on the reverse engineering scenario. I loaded back into a Save game and when leaving Boston south I'm stopped by a red signal, with no train in my way before my next destination and there is also an AI train that has been stopped just before entering Boston South.
Saving is notoriously buggy in TSW. It will affect AI trains and the dispatcher to the point where you can't complete a service or scenario. So it's best to try to not save during a run if you can help it.
