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Here are the helpful answers I received, broken down into categories.
Richard Paul
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MIGHT BE CROHNS
-It is possible to have more than one GI illness - in this case, possibly Crohn's disease in addition to celiac. The new symptoms you describe sound alot like Crohn's. Diagnosing it would require a small intestinal biopsy. It may come to this.
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MIGHT BE COLITIS
-Ask your doctor about colitis - there are many different types.  One type is collangenous colitis and it is the colon losing its ability to reabsorb the water used in digestion, therefore causing watery stool.  

-I had this same problem so my GI doctor did another colonoscopy and took  biopsis  and found out I now have microscopic colitis, the symptoms are the same.

-I, too, suffered from diarrhea a couple of years ago.  My Gastro suggested a test that is similar to a Colonoscopy except not as strenuous.  It found that I had Microscopic Colitis.  Colitis is common among Celiacs.  He would prescribe some medicine--I took Asacol--for a few weeks.  It stops Colitis. 
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MIGHT BE GIARDIA
-I had a giardia infection several years ago that caused diarrhea that became more frequent, greenish and smelled "swampy
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MIGHT BE BACTERIAL OVERGROWTH

-You may have a small bowel bacterial overgrowth (SIBO).  I was diagnosed with one a year after my Dx when I had a follow up endoscopy.  a course of an antibiotic to kill the bacteria and heavy doses of probiotics (VSL#3) fixed the probleM

-I was treated earlier this year for bacterial overgrowth. I had a hydrogen breath test that was positive and was treated with flagyl and cipro for 10 days, i needed two treatments

-when I started reading your message, I thought immediately of bacteria overgrowth, but then you said you were taking acidophilus.
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GET TESTED FOR OTHER THINGS
-I am actually surprised that so many people claim to "just" be intolerant to gluten.  It doesn't make sense that our immune systems would disfunction just in response to that particular protein.  My situation certainly seems more sensible - - an immune system that reacts to many, many things:  dust, pollens and many proteins in foods. 

-my mom has been tested for celiac(which is actually negative) but while looking for that.. they found out she had H pylori issues last week

-We both removed casein from our diets.  I noticed that those few remaining problems diminished.

-Have you considered food allergy/intolerance testing by a naturopath?  

-I eliminated dairy, more specifically, casein, from my diet.  I then began to feel good again.  Then, six months ago I again started to feel sickly so I eliminated all soy from my diet.  I feel good again.

-I'd cut out all dairy and all soy (more difficult then gluten-it's EVERYWHERE). My money would be on the vit.D, however. 

-Have you checked into the possibility that you've developed additional intolerances to *other* foods besides gluten?  Google intestinal hyper permeability or "leaky gut syndrome."

-The homeo did some testing and determined that I was reacting to corn, sugar, and a few other minor things.  I eliminated those two, along with soy, (which made me feel the same way as when I ate corn) and it helped a lot.  Right now, I think I am reacting to dairy. 

-as the celiac is more under control, maybe symptoms of other problems are showing up...more noticeable.  Often people with CD, also are soy intolerant and/or lactose intolerant.  Both could cause the symptoms you are mentioning

-I had no clue and no answers why I was sick again.  Doctor began to look for other causes.  I found I no longer tolerated things purchased or that I baked with the GF flours--especially the rice, tapioca blends.  When I finally gave these up I returned to normal.

-If you have lots of gas, you may have a fructose intolerance as I do.  Some are high fructose...apple, pears.  Try just berries, citrus, or pineapple in small amounts.  
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STOP TAKING ACIDOPHILUS
-stop the acidophilus immediately. I have the same problem from it.


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