We had a boy that had diarrhea for nearly a year. Nothing we tried worked. One thing that helped a bit was taking away any feed that had molasses in it. Other than the diarrhea, he was just fine. Ate normal, drank normal, played normal. One day it just quit--no reason for starting and no reason for stopping. We did keep his tail up to keep it cleaner and had to feed him extra because he would lose weight easily. An older pony person told me that just happens sometimes and can last from a month up to a year or so.
Try the usual things....making sure there are no worms, no fever, that he is eating and drinking and active. Have vet check for other possible reasons that others here on the forum can help you with. If, after all other things are ruled out, maybe you will just have to wait. I know that is not easy--a year seemed like forever to us--especially since we wanted to show him and that was not very easy. Don't like to have a horse that has diarhhea at a show cause people worry that their horses will catch something and I don't blame them cause I think the same thing if other horses appear to be sick or something.
Good luck.
Angie
Forgot to add that our horse was about 3 when the problem started also. Also, we had him gelded during that time and it didn't change anything.