So voltage must be getting through the room stat when it shouldn't. This points to a fault with the programmer or the programmer wiringThe first is where the CH & HW are OFF at the Timer, but when the Room Thermostat calls for heat the Boiler fires up.
The only way I can see this happening is also due to a faulty programmer/wiring.The second is where the CH is ON and HW is OFF - Room Thermostat is NOT calling for heat but the HW thermostat is - this results in the boiler firing up but the valve stays at H meaning!
Remove the prgrammer from the backplate and check if you can replicate the faults.
Check out Mid-position valve operation and fault finding