When you take probiotics the normalization may progress into accustomization of the bowel flora which means that some link is still missing if the bowel movement problems pertains, you have to remember that digestion begins in your mouth, chew it well so the gastric juices doesn't need to run low because of badly chewn food.
Take digestive enzymes with betaine to help the gut regain its gastric properties, lemon water helps with this too as does pure organic apple cider vinegar and sauerkraut.
Embrace these elements and you'll do progressing.
I'm partly suspicious to the ammoniac effect, sounds like overfermenting in your bowels, maybe parasites
or Bowel Cleanse
would be in its place.