Smoke Trouble

I recently purchased a RaceME Pro for my 09 6.7 Cummins. I have an AFE cold air intake an a 5" turbo back exhaust. I noticed when driving in town, my truck produces black smoke when I\m not even driving it hard. It also puffs black smoke when the transmission goes into lock up, or randomly driving down the highway. I noticed when it does it on the highway, the turbo changes tone. When the turbo goes back to sounding as it did, the truck no longer smokes. I tried turning the programmer \"down\", but no matter what number I have it set at, it has the same problem. Is there something else I need to do aftermarket wise to my truck to correct this problem? Any and all help is greatly appreciated. Thanks.