I'm assuming this is zoned with valves. For the thermostats that do not work on call for heat they are likely only operating the valve and not wired properly to engage the aquastat/pump. When the one thermostat correctly wired to the aquastat calls for heat the pump will engage and heat will flow through the open valve. If you look on the side of the boiler there should be square box about 8 inches high and 5 inches across, typically grey and made by Honeywell. This is the aquastat, find the model number. If it's not on the outside turn the power off to the boiler, there is some screws holding the cover on. Remove them, the exposed wires inside carry power but should not be live if you cut the power first. Just be careful. The model number should be on inside cover. Look the manual up and it will give you schematics how to properly wire the system.
There is going to be some metal boxes for each valve/thermostat. typically unpainted and about 4*4*4, they may be right on the valve. They need to be wired to each other and finally the aquastat to engage the pump.
There is some examples here:
https://www.google.com/search?q=wiri...k0nalsGdB2zPM:
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There is another symptom that has existed for a long time. I will share here in case it's related. With my indirect hot water heater, if you are on vacation for a while,
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This could be related because it will likely have valve operated by thermostatic control on the tank. Same thing could be occurring here where the valve is opening but you are only heating water on call from heat with the one thermostat that is correctly wired to the aquastat.