Summary: Train wreck 1995 and a installation of a safety-first, CYA response that slows down the trains and does not increase safety.
Longer Summary: Train wreck in 1995. Maybe driver was asleep. Start installing new signals that not only automatically stop the trains when there is a train ahead (good idea and already in place), but also when going over 45mph. Trains used to go up to 55mph with no systemic problems. Drivers go even slower than 45mph because the train is automatically stopped when going faster (as you would want to do if there was a train ahead) instead of just giving a warning and letting the train keep going.
As more of the system gets these new signals, more of the system has slower trains. Thus the increase of delays that are labeled generically as "insufficient capacity, excess dwell, unknown" from about 20% of delays in 2012 to about 60% in 2017.