For the last month or so my two year old Rheem 90 Classic model #RCGA-36A2GG21XI condensing furnace keeps cycling on for a minute, the flame lights up, the fan comes on and then it turns off. A minute later the same thing happens for about 5 times. Then all of a sudden it works fine. A couple of weeks ago we changed the themostat because we thought that was the problem. It has been working sporadically. What might be causing this?

Locate and observe the status LEDs when this is occurring. They should be visible through an oval-shaped viewer in the blower access panel (2 green, 1 yellow). Note the pattern, then check the service label/troubleshooting chart on the inside of the same panel.

Thanks for your reply. I see first the 2 green lights are on, then 2 green with orange flashing, then the orange goes off (along with the flame), then the green light on the left stays solid and the right one flashes.
I have checked the troubleshooting panel but it's kind of hard to make heads or tails of what that means.
My husband has been worried because the pvc pipe which goes out of the roof does not have a cover on it. It has been snowing pretty hard and he's wondering if the water gets in there.
Thanks for any advise.
Sue

Where is the unit located? Check the vent pipe for sags that might be accumulating water. By design, the pipe should slope downward toward the unit so any moisture will run back.

The furnace is located in a closet. The pipe pretty much goes straight up. We were able to get the furnace to fire and stay on by turning it up to 90.
It is running now-the two green lights are on and the orange light is blinking slowly.

It was installed two years ago and has worked fine the last two winters.