I presume that they checked for h pylori? Did they check your levels of digestive enzymes? With digestive enzymes there would be the stomach producing ones (HCl and pepsin) and the pancreatic ones (lipase, proteases etc).
There can be a number of pathogens that harbor the gut including rogue bacteria, yeast/fungal, viruses and parasites which include the protozoa species.
You could read Jordon Rubin's (sp) book in which he got rid of a GI problem with fermented foods and other changes. Fermented foods act as prebiotics that allow healthy bacteria to grow. This could be effective if the problem is with rogue bacteria and possibly yeast but have little effect if there are parasites present.
Colostrum has a similar effect on the gi tract and provides immune factors that can help the gut. Vitamins A and D also act on the mucous of the gut. You might want to have the doctor check your Vit D levels.
Some probiotics are too specific which may not help meaning that they only contain certain species. The gut harbors a wide range of bacterial species. Kefir is a good probiotic and is favored by a number of people. I use Lifeway brand.
If this does not work then the logical choice is using anti infectives.