I have two pups with IBD. One was on Hill's ZD Ultra for years and did very well. His diet is changed now because he also has renal issues. My other IBD pup is on a home cooked diet.
Sometimes these pups need a course of prednisone. If you cannot seem to get things under control with your general vet, I would suggest a consult with an internal med specialist. You can find one at
American College of Veterinary Internal Medicine > Home
A link I like about IBD:
Inflammatory Bowel Disease - Mar Vista Animal Medical Center