Something I've been thinking about lately are poverty foods. Paleolithic people did not usually engage in food storage, but with the advent of the neolithic, people starting keeping a larder that could help them survive. Cured, pickled, canned, confited, salted, highly spiced, and dried foods are legacies of this heritage. Some would argue that many hunting societies like the plains Indians or the Inuit also ate dried meat and that's true (though they knew they needed at least some fresh meat to prevent disease), but it's a good example of why hunter-gatherers are not models of the paleolithic.
Many such foods are popular among paleo dieters from jerky to canned sardines. I wouldn't argue that all of these foods are bad, but I have had to eliminate many of them from my diet and if you are on a paleo diet and continue having problems, perhaps they are worth eliminating. Studies on them are mixed. The regions that rely on them in very high amounts like Koreans (who eat massive amounts of pickled/salty/spicy foods) and those who live in Assam in India (VERY spicy and hot foods) have high rates of GI cancers. Perhaps the dose makes the poison though. For example, spicy foods have also shown to be cancer fighters! That's confusing!
Either way, I think fresh foods are always better and if you are in the process of healing you might want to try to eat only fresh to avoid things that sick people can be sensitive to like oxidized fats and histamines. I think emphasis on fresh foods is one reason that people often initially do well on raw diets.
I eliminated spicy foods when I started paleo because of their association with heartburn, which I suffered from. I now eat spicy foods a few times a week and haven't had problems so far, perhaps because my stomach isn't so inflamed by other crap. But recently I fell in love with a heavily spiced tea and was drinking it daily. If I didn't know that spices could be a problem I might not have realized it was causing me trouble.