[Heel n Toe]

Matt, there is one more thing that could be occurring. If this is happening it is because of a safeguard built into the system to protect you from getting put to sleep permanently with carbon monoxide.

This happened to me and my first wife in our first house, and the blower kept shutting off. Some rust on one of the sheet metal panels (this panel kept the carbon monoxide separated so it could go up the flue) had, over time, thinned the metal just enough so that when it heated up, it would warp just enough to pull away from a joint or something, and the blower would have blown the CO through our ducts into our home.

This is probably something you want to have a competent serviceman look at... as you know, you don't screw around with CO.