I knew about the autoimmune connection because I had a mystery illness for 4 years prior to diagnosis. I did a lot of research during that time, so I know all sorts of tidbits about random diseases.
I just now did a quick Google search to and picked something top on the list. I'm not saying this site is the most reliable source, but it gives an explanation of why autoimmune issues could cause this problem. http://www.healthy-vitamins-and-mine...eficiency.html
"If, for example, antibodies destroy your vitally important acid-secreting cells lining the stomach through auto-immune inflammation, less stomach acid is secreted and vitamin B12 deficiency is often the result. Here is why..."
If you have access to a library database of journal articles, (free online service through most libraries) that's a wonderful place to search for information like this.