Does timer advance ok in air only cycle? If so, sounds like your operating thermostat is not cycling. Check continuity of the orange wire that runs from the operating thermostat to the timer. If good, the thermostat is not cycling either because the thermostat is faulty or there is an air flow problem. Does the burner cycle on/off or does it just stay on?

Eric

Well, here's how it works. With burner on, you have power from the temperature switch to the operating thermostat red wire, thru the thermostat to the purple wire and onto the gas valve coils via the hi limit thermostat. When the operating thermostat opens, power is transferred to the operating thermostat orange wire instead of the purple wire. This turns the burner off and applies power to the timer via the orange wire. Timer should advance while burner is off. So, you need to determine if the burner is cycling on/off due to the operating thermostat as it should or is the hi limit opening when it should not or are the gas valves intermittent. If your not getting power to the orange wire when burner goes off, it is apparently not the operating thermostat that is turning the burner off.

Eric