I also use controller; I used to have a similar issue with my 360 controller when it was pretty old- I would just carry on running even though I was no longer pressing the thumbsticks. When I got a new controller the problem solved- the fact that you are still having that issue with a new controller is odd.
I have had "creeping" before with the camera angle where the sensitivity is set slightly too high and the camera angle will creep upwards on its own without touching anything. I know you say that you have calibrated it within the game, but have you tried turning down sensitivity to see if there is a difference?