Trane furnace pilot wont stay lit

This is a tough one without being there to see it.... The only thing that I can come up with is that you have a 2 stage or modulating gas valve and that when you have your thermostat set at a constant temperature your furnace is only operating on the 1st stage gas flow, but when you bump the setpoint on your thermostat up to a higher setting then the 2nd stage or higher modulation is called for and therefor a higher gas pressure is admitted to the main burners. This second stage pressure may be set incorrectly (too high) and causing the pilot flame to be pulled away from the thermocouple during the heating cycle which will cause the pilot thermocouple to cool off enough to cause the pilot safety to shut down the main gas valve and pilot burner. One other thing could be that if you do have a 2 stage or modulating gas valve and the main burner is shut off before the gas pressure is stepped down to the first stage then the sudden main burner shut down could cause turbulence and be snuffing out the pilot at the end of the cycle. This shut down could be from numerous things like a high temperature limit or other safety device shutting down the main burner while it is in the higher stage burn.

Fixed! Turned out, it was an issue with the condensate drain line. I had moved it and it had become just ever so slightly raised, so that the line had become double trapped. The collector was filling up with water, and tripping the secondary pressure switch.

The reason I wasn't getting a code, was because the water was gurgling, or bubbling, as the negative pressure pulled the water back up the condensate line. This caused the pressure switch to fluctuate rapidly, which is also what caused the sputtering flame problem. This rapid fluctuation, which was picked up by a multimeter, was too fast for the control board to actually register a fault.

Fixed the condensate line, and all is well.

Haven't been able to explain the cover on/cover off phenomenon, may have simply been coincidence. It ran all night, all buttoned up, without issue.