Keeping Trains on schedule

I often wonder why it's so difficult to keep the Marta trains on schedule. After all,

• the track is a known finite distance
• the average speed can be set on the train by the operator
• and the delay at each station can be set for a fixed period

It's maddening to miss a connecting bus by 30 seconds, then have to pay a 45 minute penalty just because a train was off schedule.

I also notice that the train operator will sometimes stop the train just prior to arriving at a station. This is usually done to keep the train "on schedule" if the train was arriving early. But what sense does that make? Instead of waiting on the track outside of the station, pull into the station and allow the passengers to enter/exit the train. I've missed my connecting bus as a result of these unnecessary delays as well.