I am not a doctor or anything but I would assume that the disease was there (probably from smoking, or faulty diet) and once they stopped it was more noticeable once the body is starved of it's offender and the healing process started. Once the culprit toxins are taken from the lifestyle and are not being replaced then it is withdrawal.
I would think that this is a healing process more than a cause of colitis etc. When you go back to smoking and it clears up, it should be an indicator that it is keeping it in check for you until something serious festers. It wouldn't be healing, it would be masking a more serious problem. My opinion only.