I had a similar experience over a 15 year period. I did H. Clark's programs, got out thousands of stones but even though I felt better I still had digestive problems. Eventually I found out that I had an autoimmune form of gluten sensitivity, Celiac Disease, and the only treatment is to follow a strict gluten free diet. See http://www.Celiac.com
for more information.
There are other intestinal problems that doing cleanses and taking supplements won't cure. You might want to have a complete evaluation by a gastroenterologist.