I do not believe it is a timing issue, but an issue with the automated traffic control system at the intersection not detecting cars on Mt Vernon Street. I believe the camera is improperly positioned to see traffic on Mt Vernon and since it does not detect traffic, the Mt Vernon cycle is skipped. Living on the street, I quite often see the Mt Vernon light cycle skipped and it is usually occurs when the first car in the queue is not pulled far enough forward or is making a left turn. If you look at the camera on the traffic light, it looks to be pointed almost at the sidewalk nearest to cars making a right hand turn.

Traffic will back up until the car pulls forward or gets fed up and runs a red light, which advertently trips the detection for traffic on Mt Vernon and then the light goes green the next cycle.

While, I do think the changes made to the light cycle help the situation, (especially the elimination of the 20 sec walk cycle every minute when very few people cross Broadway there). a Few issues need to be addressed.
1. Fix the traffic detection for Mt Vernon street as it is clearly not calibrated correctly.
2. The Lombardi Way stop for the light is too far back and down the hill. First, it takes longer for the first car to go through the intersection and second, cars running the red light when it just turns delays cars in other directions longer since they have to travel longer to get through the intersection. Also, since it is further back, it is slightly down the hill which causes the headlights of cars on Mt Vernon street to be in the eyes of the driver first. There is no reason why the crosswalk and stop line cannot be moved up a car length. Broadway is a one-way at that point.
3.. The stop line for Broadway traffic heading south is also way too far away from the intersection. If it was closer to the intersection more cars would be able to get through a light cycle. Also, having the stop line so far back, is dangerous when cars are trying to beat the red light. Let's be honest, we live in Boston, people often run the first few seconds of heavily congested intersections. Cars traveling down Mt Vernon Street are blind and hidden by the plywood store from traffic coming down Broadway until they are entering the intersection. Creating more of a delay for a driver to clear the intersection when lights are changing is increasing the chances that someone will get T boned on the driver side at the intersection.