I went through this with my youngest dog, who, it turns out, has IBD (Inflammatory Bowel Disease). After many treatments for parasites and bacterial infections that didn't solve the problems, many changes of diet, and no end to the periodic bouts of diarrhea, we finally had him evaluated by Dr. McConnell, the consulting internist at Friendship:
http://www.friendshiphospital.com/about/consultants.html#mcconnell . Our pup had a colonoscopy to confirm what was going on in his gut – a procedure requiring sedation, but, as it turns out, well worth it for a clear diagnosis and a way forward. Under the vet's supervision, our pup for several months had a diet of *exclusively* sweet potato and low-fat cottage cheese. I am not kidding. Bright orange poops, but a complete end to the diarrhea and upset tummy. After a followup with Dr. McConnell, he has now transitioned to a dry venison-based diet and is doing fine. He also gets periodic Vitamin B12 shots. The change in his health and in our lifestyle is incredible. I was skeptical of the whole workup and weird diet routine, but compared to dealing with diarrhea and constantly trying to guess was wrong this time, it has been SO worth it. I would STRONGLY recommend seeing if you can get a consult with Dr. McConnell.