One other thought i had late last night was that if the coal has a lot of fines it may cause burn issues. Although that seems to cause the fire to not burn hot enough, not sure if that would cause exhaust to back up into the hopper.
Do you have moisture on the underside of the hopper lid when you see the smoke at the bottom of the hopper? I am guessing that you do since that is another symptom of exhaust heading out the hopper. I'm not coming up with anything else to check...maybe someone else has better ideas?
