I have a 92% Trane XV90 and it was making a odd noise when the exhaust fan was running. It would run for a while and then turn off the flame and exhaust blower with the main air handler blower staying on.
Turns out the condensate line was plugged coming off the exhaust blower. The condensate line off the heat exchanger was flowing just fine. I pulled off the hose plug from the blower and it leaked out all sorts of water. I bet it's got a water sensor that was getting tripped. I'm surprised that it didn't log that failure as a failure code. The furnace must have been doing this for months! It just turns off the heat, restarts the heat and then repeats.
Now that it's un-plugged I can actually see water flowing. Before I saw some moisture in the line so I didn't suspect a problem..