I'm pretty sure the Juaniata has the "triburner" mechanism. What is happening is very normal for it. It can be improved. The "problem" with the triburner is that the combustion fan only blows while the burner is stoking....that is... if you stop the bed the blower would stop. On these the bed usually doesn't stop, but, as you slow the stoking down (so you don't roast yourself out) the fan slows down with it. Less fan equals less air, less air equals a burn that isn't complete. You'll find on very cold days when you ask the stove to run flat out that you get much less unburned coal because the fan is running full speed.
The cure is to remove the squirrel cage blower from the tri-burner and add a fan that runs full speed 24 hours a day. Here's a good fan: http://www.grainger.com/product/DAYTON- ... vc=IDPRRZ1
Attached is a picture of how one was added.
Also.... if you do a search on the forum for "reading upgrade" I think you'll find some posts showing this idea. Maybe someone has the posts saved and will post links to them?