Red1ton, I have a BD exhaust and pull my 5er regularly. It's about 14,000 lbs.
First, when I know my speed will be under or right around 30 mph (getting off the interstate to fill up, pulling in for food, going into a rv park, etc) I turn my BD brake off.
Second, after my BD exhaust brake had been in place for several months I had the same problem you're having, when I came to a stop with the BD brake on and then tried to accelerate, my truck would stall. It got to the point where my truck would stall (even with the BD exhaust brake off) when I was backing my 5er into a spot at a rv park.
I came to this board and was asked what to do. Simple, my idle rpms had gotten too low. I turned my idle up to where it should be then no more problems.
I suggest you do a search on "adjusting idle" or something similar. You will see good info. It's not hard to do... and I am not a mechanic.
Bill Cook