The thermostat, will be connected via 2/3 wires. All boilers are designed to take all variations of thermostat connection. SO disconnect it. Usually shown somewhere, and your installer should have left information about it. After disconnection of it, boiler should then be on a manual control, no temperature control. All should then be ok, boiler off unless you turn it on. Which will show that problem is with controller. Or not.
SD
September 2012