William Walsh of the Pfeiffer Treatment Center thinks it boils down to oxidative stress in the gut.

http://www.gatago.com/sci/med/nutrition/9952267.html

http://asa.confex.com/asa/2005/techprogram/S1181.HTM

Instead of thinking that gluten issues are behind other conditions like auto immune problems, it may be that one thing is behind those two things, both gluten sensitivity and auto-immune problems.

I think there may be one thing that is common to all sufferers, one thing among those with gluten AND auto immune problems. That one thing may boil down to oxidative stress in the gut.

The GI tract is important; if there is any damage the effect it has on the whole body can be pretty far reaching, causing problems with anti-oxidant levels for one thing. But I think it may be possible that if these anti-oxidant levels stay low long enough if may cause other problems too.

Oxidative stress and autoimmune problems.
http://www.lef.org/protocols/prtcl-017.shtml

Autoimmune means the body is attacking itself. Usually the first place this can start is with foods not digested properly. The body attacks these foods that are not digested completely, beginning the cycle of autoimmune problems. Why do the foods not get digested properly? Different problems but damage to the GI tract may occur because of the lack of anti-oxidants over time, I guess.