You do want mode three, which you've got correctly. You definitely don't want your fuel/air/temp trims set to 6/4/1, that's for the PDVC stove. If you've got a really good exhaust and a perfectly clean stove it might run ok like that (and give off tremendous heat), but if it's set like that, it's probably gonna run way too rich and give a dirty burn. The factory settings for the PAH is Low Fuel Feed at 1, Low Base Air at 4, and Air on Temp at 1. To adjust these, with the stove on, press the button you want to adjust. Then press both the blower and heat level up or down bottoms at the same time in order to raise or lower these settings. You'll want to make sure those trims are right.
Let's talk a little more about your setup, What is your venting, both intake and exhaust? For example - my PAH has the factory 2" flex hose feeding the stove outside air. The exhaust consists of 3" piping, beginning with a 45* elbow into a 90* elbow taking the exhaust path vertical through 30" of pipe. Then another 90* elbow take the exhaust back horizontal for 24", through the wall, and terminating outside. How long have you had this stove? How much have you burned this year? When did the problem start? What heat setting are you running? Using a thermostat, and if so are you running high/low or on/off mode?
This stove is pretty particular about how you clean it out, especially if you burn it dirty and load up the heat exchanger. I've found that the best technique is to clean out the entire fire box area first. Then I remove the clean out plates and vacuum out what's inside. Then, I take a wooden mallet and beat on the heat exchanger wall (back of the fire-box - wall where the pellets drop out). I don't beat it like I'm trying to break it, but you need to be fairly vigorous. Keep beating until stuff stops falling down into the clean-out ports. Vacuum it up, and then bang on it some more - it usually takes several minutes of beating and vacuuming to really get it cleaned out right, especially if you let it burn dirty. I usually get 3-4x more material out than what is laying there when the covers first come off. You also may need to pull the combustion blower and clean that as well - there are really good video instructions on Englander's website on how to do this. Before you start - you may need to replace the combustion blower gasket, so make sure you have a spare, or a suitable gasket making material to replace it.
Having that heat exchanger clean makes a tremendous difference on how the stove performs (assuming you have no other air leaks). If everything is truly good and clean, we can look at some other suspects.
