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What is the model number of your boiler? You can bypass the thermostat by connecting the 2 thermostat wires together
When there is a call for heat the burner will run up to the limit set point then shut off but the pump(s) will continue to run until the thermostat is satisfied. If the call for heat is long enough the burner will come back on when it drops below the differential setting on the control. If your boiler operates this way then it functioning normally.
I don't know what you mean by an in line water heater. Do you mean you have a DHW coil in the boiler?
Ok, it will take a while for the tank to heat up. 1 problem thermostat should not affect the other zones. So if you had no heat in all the zones you had/have a problem other than a thermostat problem. What is the brand an model number of the zone control with the lit LED's?
Just because the burner shut off doesn't mean the heat shut off (see my previous answer about system operation). If the boiler is near 180 degrees then shutting down is behaving normally.
You need to check the temp gauge on the boiler. Is it near 180?
Ok what light is flashing on the boiler control (not the ZVC)?
You have to remove the front panel to the burner compartment
Sorry, the top panel will give you a better look
Ok, you need to have a pro check this out. The control is indicating a flame failure problem. This probably isn't something you can handle yourself unless you're comfortable working on a gas appliance. Let me know if you want to pursue troubleshooting this yourself.
Ok, turn the power off wait a minute then turn it back on again. Tell me what happens. Does the draft fan run? does the igniter glow? does the burner fire up then go out?
Ok, this model, particularly as it ages, has a known issue with the burner cone. I suspect that's the problem if it fires up then goes out. Dealing with a burner issue is not a DIY project
I'd suggest you call in a pro who is familiar with this model. He'll have to pull the burner assembly apart and check it out.
It's a bit involved could easily run $4-500 hundred (maybe more) depending on what he finds.