If a newwer furnace has an issue with the heat exchanger it is definately a major problem. It does not take much for the furnace to start sooting up from an impropper air fuel mixture. A combustion analysis will tell you if there is an issue with the heat exchanger. Oxygen, carbon dioxide, carbon monoxide, excess air, and efficency readings should be within range. Any air being sucked in the crack instead of the primary inlet will cause issues.