In order for the beacon command to work well with the train, it must be specified in the route file what system will you be running. On top of that the ATS system must be installed properly on the train itself. For example if you check out what Rayvon did with the Riverbank Park Shuttle you will see what I mean.
If you look at the beginning of the route you will see the change.route command, and you will see the beacon command displayed through out the route.