Maybe you've healed your gut with Paleo awesomeness.

As a test, my wife's doctor took her off gluten for a month because she had been having GERD problems for quite some time. Suddenly she could drink coffee too with no acid problems.

Coffee contains a variety of tannins and acids that are bitter and astringent and can be quite irritating to the lining of your gut. Black tea and dark chocolate are similar in this regard.

Adding milk or cream to coffee, tea or chocolate effectively neutralises the effects of these compounds making the products more palatable for most people.

However you can become used to these compounds over time. Many people can gradually work their way up from milk chocolate to very dark chocolate that would previously make them feel sick. Your gut becomes accustomed to experiencing the bitter compounds and learns that they are not actually harmful.

In the same way if you drink no coffee for a few months and then drink a strong black coffee you may experience the same stomach upset again.

At least that is my theory.

I could also speculate that by reducing the the amount of sugar you eat your body becomes more accustomed to the opposite bitter, acidic flavors.

It is also possible that the lining of your gut now has greater integrity and a better layer of mucus protecting it.

When I first went paleo, I discovered pretty quickly that it gave me an iron stomach, compared to what it was like before. I've gotten used to it now, listen to my gut more, so I'm back to being leery of some foods, but at a whole different level. No more acid reflux, no more indigestion, just intestinal grumbling.

Going Paleo/Primal shifted my metabolism from sugar-burning to fat-burning, chiefly by jettisoning grains fand feeling fantastic as a result. I never had a craving for sweets, but now, per se, I seldom even register a taste desire for sweet stuff, especially mega sweets of the desserts kind. (My diet includes fruit yet not in the sense of "needing" it in sugar-rush sense, because, probably, protein and fat in my diet keep my blood sugar stable.)

Anyway, my point, and I do have one, is: post-grain living seems to have heightened my appreciation for bitter tastes in general. Pre-Paleo, I can't say I disliked black coffee, but seldom drank it by choice. Now, even though I'm not averse to a cappuccino with foam, I find myself really enjoying the bitter of deep, dark coffees. Add a chunk of ultra dark chocolate, and I'm a happy camper. For what it's worth, my appreciation for sour tastes (as in sauerkraut) and hot tastes (chili peppers, full range) is also up.

I'm not quite willing to call my shift away from grains causal in all this. But if find it correlative in an interesting way.

Now that you mention it, I can drink my coffee stronger and blacker than before, and more of it, with no ill effects. I got peptic ulcers a while back and tracked it down to coffee intake (coffee, not just caffeine). That was when I was on a SAD diet. Now that I am Paleo, I never have sugar in my coffee, just some cream, and can have 3-4 cups a day with no stomach problems. Interestingly, the caffeine does not affect me as much either, I never get jittery or lose sleep.

Generally my stomach is much tougher in some ways, like this, but also is much more sensitive in other ways. Like I have become very sensitive to vegetable and canola oils, to the point that just a few bites of food cooked with that has dire consequences.

Going low carb makes things you didn't think were sweet show up as sweet. Case in point, I started with unsweetened coconut before going paleo and low carb. I didn't taste any sweetness at all. Now it tastes sweet to me. So our tastes and ideas of what's too sweet, too salty, etc. adapt.

Going paleo heals your gut, and provides (hopefully) the right amounts of minerals and other micronutrients after your gut is healed, this allows your stomach to return to proper acid levels. Contrary to Conventional Wisdom, GERD/Acid Reflux happens when your acid levels are too low. This is because bacteria will overgrow in this case, causing added gas pressure, pushing the acid upstream.

Once you're healed, these issues go away and "trigger" foods don't have the same reaction.

Sadly for me, it's caused by dairy, and even after repeated retries, it sort of comes back when I try it, so I think I won't be able to really use it. But I can get away with small amounts of dairy for short periods of time (i.e. 1x-2x/week, but regular use and it's acid hell again.)