I have had some of my meds pass right through too. that can be discouraging. However, ask your doctor if some of these non-soluable, or non-digestable meds are available in liquid form. That is what my doctor did for me, and I actually began to feel so much better, because I was actually finally benefiting from them. when they come out the way they went in, it is kinda obvious that we arent getting the medicines absorbed into our systems I guess. The only advice I can really give you is to make sure you try to tell your doctor everything that goes on with you, like any pains, the foods you are eating and drinking, how you feel at different times of the day, etc. (I keep little notes to myself when things occur, so that when I see the doctor I can tell him) I know usually when I actually get in to see my doctor, I just seem to go "blank" and cannot be thorough in describing things to him or her.
I really hope this helps a little. take care, I will keep you in my thoughts. Please let us know how you are doing, and if any of this helps. good luck now.