I had a Kerr TW2000 for about 15 years. Mine, too, puffed sometimes. When the wood load was early in the burning stages, and there was lots of gasses coming off, and the damper was closed down, I'd get little explosions that would make the damper kick open and spew out a nice handful of ash, dust, smoke and sometimes a flame. The first few times it happend, and I heard/smelled it, I sat there like a dummy watching it, with my face just a few inches away from the damper. POOF! I leaped back, hitting the wall, and spitting ash. Had to take a shower!
The manufacturer offered no solution. I figured it was just an oxygen starvation situation, letting the combustive gasses build up until they exploded, instead of burning them off slowly in a controlled manner. So I drilled a little hole, about 3/16", in the centre of the damper. Just that little bit of air flow stopped most of the puffing / explosions.
And I didn't put in a big load of wood in the boiler when I was near my max temps, to avoid the idling with fresh firewood that was the biggest culprit of the puffing.
BTW - I don't believe my situation had anything to do with house air pressure or chimney draw. My chimney is 32' of 7" stainless steel, and it draws cleanly and consistently. I don't have smoke rolling out of the boiler when I open the door.
One more thing: I was not happy with the how the TW2000 held the damper open until the high temp was reached. I felt once it got a roaring fire going, it dumped a lot of hi temp exhaust up my chimney. So I installed an adjustable 10 minute timer in my damper circuit, and set it for about 7 minutes. So when the system called for the damper to open, it would open for 7 minutes, then close for 3. As the fire got roasty hot from the draft being open for 7 minutes, it then shut down for 3. I got more hot water during the 3 mintues of damper shut down than I did during the 7 minutes of damper open!
Good luck with your system.