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Tim,
Your experience with baking bread sounds identical to mine this past
winter/spring!  It WAS the tapioca flour, purchased from Dietary
Specialties, as I discovered after months of checking out the xanthan gum,
yeast, etc. etc.  Since I switched to tapioca flour from the chinese market,
I haven't had any symptoms.  It might be worth a try.
 
Various helpful celiacs advised using methocell (I think Ener-G sells it).
I never bothered, after I discovered the tapioca flour problem.  I did try
guar gum, but it definitely causes the runs for me.  A half and half
guar/xanthan gum mix works OK and doesn't seem to be enough to cause
digestive distress for me, but things might be different for a 2 year old.
 
Good luck!
 
Laura
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Ithaca, NY, USA