--there's a lot of info out there on your second question--anything I could say would be pure speculation (though gluten problems are known to influence a host of bodily processes).

As to the first, though, there is some degree of controversy regarding exactly what "standard" gluten tests show.

The current gold standard for frank celiac disease is villious atrophy seen in biopsy of the small intestine. Celiac is notoriously undersiagnosed this way, though, as one can be testing during an early stage of the disease before there is much atrophy, or the samples can be biopsied from an area where ther is not yet obervable damage. (This is why some advanced gastric specialists really like to try the capsule camera approach--but that canb e hit or miss, too.)

One other indication of frank celiac is the skin condition dermatitis hepatiformis, which involves skin lesions with IgA deposits--there is some evidence now that other conditions might also result in such lesions, though.

Among the blood tests, given a "normal" level of IgA antibodies (some people have IgA deficiencies), the anti-transglutaminase IgA assayis suppoed to be most specific for celiac, in that it seems correlateed with degree of villius atrophy. However, a full celiac panel also includes the anti-gliadin IgA and IgG assays. Depending on whose opinion you read, the anti-gliadin IgG test is the least specific, but most sensitive test--there are a number of people without gastric symptoms but neurological symptoms who seem to show up with isolated positive anti-gliadin IgG results.

There are also several other serological tests in the works that haven't yet gotten widespread dissemination, that JCCglutenfree knows a lot more about than I (got to get her to come over here and comment).