I have the exact same problem. We had the company rep here and he said it happens when the system starts up at low flow rates because it just doesn't need as much energy so it doesn't burn clean. One issue we have is that we are on a well, but I also find it happens when their circulation pump runs. His final recommendation was to go out the chimney as long as it isn't over 100 feet. I suspect that I will go with that option eventually, but I am also concerned that the incomplete combustion is killing all of the efficiency benefits I may otherwise have gotten. It's very frustrating but everyone from the company, at least, doesn't think this is a problem.
Have you gotten any satisfaction yet.