Before our first winter, we hired a plumber who was certified to work on our type of boiler (and who was recommended) to make certain everything was working properly. He was the one who pointed out several of the issues, such as a water heater whose controls face a wall and a thermostat for one zone which is directly above the heater for a different zone (we have five zones in the house--three upstairs and two downstairs). He told us that fixing these issues would require a large (and expensive) amount of modifications. Instead, he helped me balance the thermostats so that they would still function and give us the heat we needed.
Unfortunately, this often left the boys' room running very warm. Somehow, it was getting heat pumped through even when its zone was turned off. Meanwhile, the living room heat also seemed to have a mind of its own.
Recently, our boiler's maintenance indicator came on, including a telephone number for a different plumbing agency--presumably the one that installed it. Yesterday, the plumber came in and fixed nearly all of the problems. Sure the dining room thermostat is still above a heater controlled from my bedroom's thermostat and the water heater is still facing a wall like it's in timeout, but the rooms now are heating correctly (which is especially nice in the boys' room).
It took the plumber about five hours of hunting as well as fixing or replacing about five different components which were causing the problem. The bill was like buying a new appliance, but the difference is quite noticeable. Hopefully, we'll see the difference in our heating bills.