The first thing that I would check is to make sure That the power supply to the furnace has its ground wires tied to ground. The furnace should be on its own circuit from the breaker box and all grounds tied in. If it starts up without sputtering, I would think the flappers are doing there job. When a flapper sticks it usually starts to sputter or miss. Next check outside and see if the exhaust pipe is longer than the intake pipe. If the exhaust gases are going into the intake pipe it will shut the furnace off. One way to check this is to cut the intake pipe at the furnace and see how it runs. It will sound louder than normal, but it wont hurt anything. If it works fine this way, you either are recirculating flue gas into the intake or the intake is restricted. I have had wasp nests in the intake pipes that will do this at times. Bigger nests will turn inside the pipe and sometimes stop where it closes off the pipe. You can suck them out with a strong shop vac or blow it out with compressed air. They should have changed the spark plug and sensor wires when they changed the control. They should both be orange in color. Also make sure the drain is clear. It should have a pressure test done on the heat exchanger as Lennox wants all pulse furnaces pressure tested every 4 years.