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Seems that I have a gas furnace that is having some sort of heat/air sensing issue.

Basically it shuts off after running for a minute or two. But if I remove the top plate of the furnace itself it runs just fine.

It has an automatic ignitor which is doing just fine. Also no errors on the motherboard. But as soon as I put the top plate (area of ignition and flames) back on it will short cycle on me.

Too many registers closed? I just cleaned the filters out so that isn't it...

More Info: Model - will get the exact when I get home but its a Rheem high efficiency model bought about 5 years ago.

Any recent changes - Finished basement 3-4 months ago and added to duct lines - the duct lines have been up 5 months.

Can I see pilot light? There is no pilot light since it is automatic ignition. The ignition is working fine. Flames come on strong with cover on or off - so don't think it is a gas issue and I have several other appliances with no gas issues. With cover on it does seem like there is a grasp for air eventually (after a couple minutes). I can't see the flames with the cover on but it seems to go through a normal shut-down and cycles back on in a few minutes.

Filter - Filters are brand new.

Does the blower run when unit is off? No. As mentioned before I can't find anything odd except for the short cycling and the what it seems like lack of air.

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The two PVC pipes meet about 4 feet above and go out the back of the house. The one on the left is always a little warm and the one on the right cool. There doesn't seem to be anything obstructing the pipes but I also did the "paper" test while the furnace was on and it didn't suck the paper in. Today was about 20 degrees here and I could notice warm air coming from the pipe outside (not blowing but you could tell).

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This is with furnace door off. Everything seems to be working fine. Has electronic ignition so no pilot.

Other note: We have an electronic air filter that has been turned off for a while because of some construction we are doing. Found out today that it is dead. Shouldn't matter to the furnace but who knows.

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    Is this a high efficiency furnace? Have you checked if the air intake pipe is clogged? – Edwin Jan 21 '14 at 1:23
  • The air intake is just about 10 feet of PVC out of my house. It is only about 4 years old and has a screen so not sure how it would be clogged. Any good way to check the air flow is right? – DMoore Jan 21 '14 at 1:43
  • I don't have a good way. Maybe a sheet of paper outside when the unit is on? The reason I ask is because when the door to the combustion chamber is open, there is typically unrestricted combustion airflow. When it's closed and properly sealed, the combustion air comes from the intake pipe. The other thing to check is the draft inducer motor. – Edwin Jan 21 '14 at 3:31
  • @Edwin - will try the paper out tomorrow. Thanks for the help. Spent 3 hours troubleshooting it today because an iffy thermostat that batteries died happened at the same time. – DMoore Jan 21 '14 at 5:03
  • Supplying the make and model of the unit is usually helpful. What have you checked during your 3 hours of troubleshooting? Did you make any changes, or do anything just before this started happening? Posting a video of the furnace operating abnormally would be helpful. Can you see the burners and/or pilot with the cover on? If so, does the flame get smaller before the furnace shuts down (or act as if it's starved for air), or does it go from full blast to nothing? Have you checked to make sure your gas pressure is good and consistent? How often do you change the filter? – Tester101 Jan 21 '14 at 11:45
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Had a similar baffling problem. Called in a pro who checked out everything and he discovered a clogged condensate tube. Water backs up into the secondary condenser fan and gets into a vacuum pressure tube. With a little water in that tube, the vacuum level is way off normal and the safety features kick in and the burner shuts off. Solution was to "blow out" the clogged tubes, drill one of the tube orifices out slightly (from a diameter of about 3/16 to 3/8), reattach the tubes and everything seems to be working.

This also explained why turning the system off for about 10 minutes seemed to work for a short time each time. The water would drain out of that fan and from the pressure tube so everything would start fine. But after a few minutes, condensate that was being created would back up and cause a shut down.

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It us useful to understand the basic operational logic of these new furnaces to be able to pinpoint possible problems. On high efficiency, direct vent furnaces, when the thermostat calls for heat, the inducer fan turns on. If the vacuum sensors do not sense sufficient draft, the whole thing shuts down. If it is starting correctly, the intake/exhaust is not the problem. The next thing that happens is the igniter turns on for a while until it glows hot, then the gas valve opens enough to light the pilot. If the igniter did not get hot, the pilot will not light and the heat sensor down wind of it will not sense heat, the whole thing will shut down. This is not your problem, either. If the pilot lights and the flame sensor reacts, the main gas valve will open and the furnace will fire up. When the air in the plenum (the box the ductwork attaches to) gets hot, the sensor there will turn on the big blower that sends the heat around the house. If the fan came on before the whole thing shut down, this is not your problem, either. If that sensor is broken or the fan doesn't work, the furnace will overheat and the overheat sensor will shut it down.

I had the exact problem, and walked through the sequence as above. The answer is above in another answer. The condensate line was plugged. I could see water in the clear vinyl drain lines. (there are several of them that sense the vacuum in the various areas of the furnace.) In my case, I tracked the main drain line and found a trap in the line. I disconnected the hoses and removed the trap which was plugged with 20 yrs. of dust and misc. gook. Gave it a good brushing and flushing, reassembly and all good. Water was draining slowly through the guck so it would start after a rest, but when the water started coming, the drain line would fill up quickly. I had a little trouble figuring this out, because there was water coming out the end of the drain pipe, just not fast enough.

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I would look at one of two issues, plugged condensate tubing as was mentioned, as well as plugged or sagging exhaust/intake venting.

Frost can build up on the exhaust/intake terminations

Sagging or incorrectly sloped intake/exhaust can collect water

but more thought, these are less likely due to working fine after resting but none the less other possibilities: faulty pressure switch, leaking pressure switch tubing, an eroding combustion blower wheel, worn bushings in the combustion blower motor, leaves in the intake screen at the furnace, corrosion in the heat exchanger, faulty gasket between combustion blower and HX, incorrectly sized venting

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This isn't a great answer but I want to provide something in case it helps others.

There was no issue with my flame sensor or the ignition device. It went on just fine but was kicking off due to some other reason.

After a lot of troubleshooting it was fixed by one of three reasons:

  • powering off the furnace for a couple hours with thermostat disconnected.

  • installing new thermostat. I was due for a new thermostat and not sure what could have been wrong with the old one. It did run out of batteries right before this but it doesn't make sense that when I left the old thermostat it worked fine with the furnace cover off. The only thing I can think of is the old thermostat was sending incorrect signals to the furnace that caused it to need more air during usage (maybe an AC expert might be able to give a plausible reason for this).

  • Reseating cover with slight gap. I have since put this fully on but left it with a slight gap the first couple of weeks.

I did nothing else to the unit and the unit was in otherwise pristine condition - only a couple years old.

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