First off, I would make sure that the combustion fan is blowing at 100% all the time.
To do that while it is doing its normal thing, unplug from the coaltrol and plug directly into an outlet via extension cord. If you notice any difference in the height of the flames, that should indicate the blower not at 100%. Or if you can hear any noticeable change in the speed of the blower. Try leaving it plugged directly into the outlet for a day and see if you notice any difference.
You mentioned that you cleaned the air holes but have you run a drill bit through them to make sure they are completely open ??
It MAY be that the combustion fan needs cleaning or oiling, or maybe it is getting tired.............