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I have this problem when I drink sometimes. For me it has to do with me being hypoglycemic (the opposite of diabetic) and the sugar content of some beers. Your body is dehydrated, and your sugar level is really high. What you can do to prevent most of it is to drink a glass of water between brews it will help.
Natural sugars (apples, oranges) have the least effect on me, processed sugars (the stuff you use in your coffee) have the biggest effect of all (I use honey in my coffee). So if a macro brewery uses sugar to "boost" og (they wouldn't do that would they?), I am affected, though I (not to date anyway) have not been affected by any brewpub in this way. I don't/can't drink sodas because of the sugars in them (Coke makes me want to sleep & gives me a headache... e.g. hangover). I stay away from candy bars most of the time.
This is the biggest reason I'm a beer drinker, Mixed drinks, like bourbon and coke, ruin my whole night. The sugars from the malt are "natural". Bourbon is "natural" also, but I can't drink it straight, or with water, and the concentration of sugar in fountain sodas is higher than bottles ones. I don't care for the flavor much in the first place.
The leading cause of headache production with any fermented beverage, consumed in moderation, is the ingestion of higher alcohols. The easiest way to produce higher alchols, is to under pitch your yeast. There are some very striking commercial examples of under pitched beer. While attending a brewing class at the university, they served many of these beers, during tasting seminars, so we could learn to appreciate the flavors produced by these compounds. Probably the most dramatic improvement a homebrewer can make in their brewing is to pitch adequate amounts of healthy yeast.