Ammonia is a waste product of protein metabolism I believe. Ammonia should get neutralized in the liver and then excreted through the kidneys and urine. It is possible that one or some of your liver detoxification pathways are not functioning properly. You can get a liver detox profile done by a place like great smokies lab in north carolina (you'd send away for it), or you can just try a diet that is beneficial for the liver and see how it goes.