Something just don't add up, I'm not questioning your results, but just trying to figure where the problem is.
While the PB will come out dark, 2oz's of apple wood shouldn't give it much of a smoke taste, especially after pulling and mixing it all together.
I'm wondering about the wood and if there is not a problem with it? Did you get it from CS or buy it somewhere else? Does it burn all the way up? What kind/color of smoke comes out of the exhaust hole, say 1-2 hrs after starting the smoker?
2oz's of wood on chicken is plenty, but on ribs and butts it shouldn't have the burnt house odor.
How big was the butt and how long it cook and at what internal temp did you pull, just trying to figure out if the smoker is cooking/reading the correct temps.