If the water does not drain properly out of the secondary heat exchanger, flue gases cannot travel though easily, and the combustion gases back up. This causes the flue gas created by the flames to find another exit – usually out the front where the gas and air entered. The errant flue gasses disturb the flames creating yellow coloring, dancing, extinguishing and relighting, or rolling out of the combustion chamber. The resulting flames often create a lot of carbon, which can further clog up the heat exchanger.
If you see these symptoms BEFORE the indoor blower is energized, you should first check to see that the induced draft blower is operating and that it is actually producing a draft. Sometimes the blower wheel comes apart or slips off the shaft – causing the motor to turn without actually moving any air. Next, you may want to inspect the secondary heat exchanger for obstruction. This varies between units, but most often you will need to remove the draft inducer to see the secondary heat exchanger. If the secondary heat exchanger is filled with water – you need to solve the drainage problem.
If it is clogged with black soot, the secondary heat exchanger will need to be changed. If that is the case, you will also need to look for the cause of the soot. Double check the orifice and operating manifold gas pressure. An oversized orifice or incorrect manifold pressure can cause soot. If the furnace is located more than 1000 feet above sea level, remember that it must be de-rated – which can mean a lower manifold pressure and/or a smaller orifice. Check with the manufacturer for orifice and manifold pressure recommendations. If the furnace uses sealed combustion (combustion air coming in through its own pipe) check to see that the combustion air pipe is not restricted. Birds and rodents are common problems. If the flame pattern is fine up until the indoor blower comes on, and THEN the flames get wacky, you probably have a cracked primary heat exchanger. In this case, the primary heat exchanger definitely needs to be changed.