The problem you have is of the two thermostats the one with the higher setpoint senses its room temperature and controls its boiler to maintain that. That means the one with the lower setpoint is always satisfied and never brings its boiler on-line. I had the same problem with the office part of my shop and the working area of the shop. The only way I solved it was to move the two thermostats away from each other so that each primarily sensed the ambient temperature at each location.

Why now? Electronic thermostats are precise to a fraction of a degree. Even with the same indicated setpoint, you end up with actual setpoints are not identical and you end up having the higher setpoint control the entire show. Between the mechanical hysteresis and the inherent inaccuracy of the old electro-mechanical thermostats I'm not surprised that it used to work.

Solutions, they have all been presented to you. If using one location for a thermostat for the entire house is acceptable, then tie the two boilers together with a single thermostat. If you want to retain both thermostats then you are going to have to get more separation between them. For my shop it took about 20' to get the job done.