Really interesting theory that it is a reaction to the clean diet.
About a month ago, I broke out in hives all over my body. I had never had hives before, and was not strongly allergic to anything (mild hay fever, varied by year/season). My hypothesis at the time was that is was in response to the handful of almonds I ate a few hours prior. Of course I had been almonds pretty much my whole life, so it was very strange indeed.
The very next day, I broke out again, this time with no almonds. I had, however, taken an aspirin a few hours prior. The hives start in areas where clothing is tight fitting, my skin gets very warm, and there is a general flushed look. I actually went to the ER because I was worried about respiratory complications (though there were no symptoms).
The hives disappear with the help of benadryl. Since then, I've eaten almonds twice as a way to test the theory, and both times have had reactions. I've read that allergies can arise and subside suddenly throughout one's lifetime.
I'm 25 yo, and had started eating primally about 2 months ago. I went primal for about 8 months last year, falling off the wagon in February 09. From then till about the end of the summer, I ate pretty horribly and gained 15 lbs. I have been wondering if going back to eating well somehow is triggering the release of histamines, but had not been able to find out by what mechanism this was happening.
I'd like to experiment with eating other tree nuts, and maybe try almonds again in a few months. Gtr, I'm sorry to say it is possible that you may be allergic to nuts, too. I'd recommend eliminating for a few, and then having maybe 6-8 nuts to see your body's response. It really sucks since I really like almonds, and at this point I'm hoping it's at least not all tree nuts.
Everything in moderation, including moderation.