If it does stop again it is possible the intake side of the flue is being subject to back pressure from improper venting outside. If it is going horizontally out it may need turned down 90 degrees.
Interesting.
The intake and exhaust come out of the wall quite close to the ground (it's a real old house), make a 90 degree turn up, then have an upward run of 2 and 3 feet and then have a 90 degree elbow on the top.