Hi Rick, many have had missing problems with the fuel management systems PC on there bikes. At least the ones I have heard complaints about, the rest love them. Anyway what I would do besides putting in fuel treatment and seeing if that cures. I don't have power commander on my bike , have done K&N filter, RoadHouse slip on and it runs great. But I still hit limiter every so often to keep carbon build up out(old Roadstar days what we did) and adding Marvels Mystery Oil to every few tanks of gas.
Ok long story short...lol... unhook PCIII, and see if it runs better. Most have found besides decel pops that the stock ECU runs good. And you will gain some fuel economy.