It could be histamines in the beer. I just did a little reading up on this for a friend. Many fermented foods (cheese, beer, wine, cured sausages, saurkraut) can contain histmines and some people are particularly sensitive to them. This IS NOT classified as being allergic to something, more along the lines of being a chemical sensitivity, even though the net result is often the same (different process though). I have another friend whose wife was tested negative for milk allergies and lactose intolerance, but many cheeses cause her problems. It's a good chance it is a reaction to histamines.
I did find one paper that says that properly made wine should not contain histamines. This paper was saying that histimines that are produced by bacterial contaminants, not the yeast. I did however see other (non-scientific) web references that says yeast are a source.
Try some lambics or other sour beers and see what happens. It could just be specific beers, not all beers. Better sanitation = less problems