I have heard people say that "dark beers" give them head aches, but I always chalked that up to inexperience and/or a psychosomatic explanation.
I suppose it is possible that the higher ester (or more likely, fusel) levels in ales could trigger a migraine. That would be the most likely explanation.
I have also heard people say that draft beer gives them headaches and bottled beer doesn't. And there is absolutely no logical explanation behind that... unless it is that they DRINK more when they aren't counting the bottles.
Bottom line, beer can cause headaches. Especially when consumed in large quantities. The worse hangovers I ever get are, without question, from Belgians. Hoppy beers seem to give me more hangovers as well. I can drink bourbon all night long and never get a hangover (though I may feel sluggish).
I once heard Mr. Jackson say that the more complex the beer, the worse hangover it gave him. And he chalked it up to there bering more chemicals creating the flavors in the more flavorful beer. That makes sense to me.