You shut the gas valve switch to the off position while their is still a call for heat. The CO rises because the unburn gas is traveling through a hot heat exchanger causing it to produce CO from inadequate combustion. Just as if you were to take a reading on a overfired furnace. Incomplete combustion. Doing the reading with the analyzer is just a easy test to perform at the end of your combustion analysis after tuning the furnace to double check the saftey of the gas valve. I would use a combustable gas leak detector if i were only there to check to see if the GV was leaking.
You should take Jim Davis's class offered by NCI. It will open you eyes. Best class i've ever taken hands down.
I am watchin CO. I never watch CO AF. Tha is just a calculation. CO is the actual reading of the amount of CO present in the flue gas..