Interesting. If you wear socks, have you already ruled out some component of your socks (latex/stretchy stuff or rayon or polyester?) or laundry soap residue that leaches out from the socks when your feet sweat? The reason I ask is that often allergic dermatitis is from direct contact (it's often called "contact dermatitis"). I realize it could be something soaking into your socks/feet from the shoes, but don't overlook any possible source. Also keep in mind that "hypoallergenic" doesn't mean "non-allergenic." It just means that most people don't react to it.  In that context, I imagine most shoe insole materials could be considered "hypoallergenic" since the vast majority of people don't react to them.

I speak from experience, although not with regard to running shoe materials... sorry!  This sounds funny but I develop a raging rash on my eyelids if there is the slightest speck of red/pink pigment in eye makeup, even if the product is liberally labeled "hypoallergenic" and even if the saleswoman insists over and over, "don't worry, we thoroughly test our products and they won't cause allergies."  Yes, they will, if my specific allergen is in it. I can wear those pigments on other parts of my face, just not on my eyelids. Obviously my problem is trivial by comparison... I only mention it to point out how puzzling allergies can be. Maybe your feet are sensitive to something that the rest of you isn't. Who knows. I would see a dermatologist next for more specialized help in identifying the cause. Best of luck!

How interesting! Hopefully it will be one of those two things, so you don't have to spend even more time and money hunting down the source. If you think of it, post the answer if you find out. I seem to have bad luck with odd allergies (the eye makeup thing, and German shorthaired pointers... lol)  so one can never be too vigilant! Good luck.

I would also like to know the follow-up since your testing, but it's easy to get stuck on the details and miss the big picture. Allergies and hypersensitivities may be common, but they are not common enough to be considered "normal," or even a version of normal health. If they were universally acquired and lost, maybe, but an over-reaction by your immune system, to something that bothers few others, can be a symptom of a problem elsewhere. Like many in this forum, I've had allergies that I eventually lost, and I believe that can happen for anyone.

The rapidly developing field of epigenetics is showing how easily DNA can rearrange itself in response to environmental stimuli. The idea that some people just react a certain way to things as a result of genetic predisposition is no longer sufficient explanation for allergies, or almost anything else anymore. You may have been exposed to, or still in contact with, something else internal or external that has your immune system fighting  things that are otherwise harmless. I wouldn't worry about it, but it is something worth exploring.