The Barefooted Lie?

It has been nearly ten years since I first started running barefoot around BYU's indoor track. Back then I ran with a very heavy foot, you could hear my shoes pounding against the ground all the way around the track. Running barefoot, as my friend Ryan Daniels suggested, would force me to change my running style and run a lighter on my feet. It worked fabulously, suddenly instead of hearing the loud THUD, THUD, THUD you would hear a soft pitter patter as I ran by.
Unfortunately, barefoot running is not as easy once you leave the indoor track. So for several years I went back to running in my old running sneakers, until Denny gave me a pair of Vibrams.
The journal of Science had just published an article showing the benefits of running barefoot and I was excited to start cashing in on those benefits. However, after running with my Vibrams I started having people come up and ask me "Have you read Born to Run?" Finally, I read the book and that is when the doubt started. The books arguments were so poorly articulated and lousy with lacunae that I started to wonder if there really was anything to the barefoot argument. Then one day while standing barefoot in my kitchen I noticed that my hip and joints were really aching. I decided to go put on some sandals, and the pain went away almost instantly. Over the next few weeks I noticed that if I am wearing shoes or sandals in the kitchen it takes over an hour of walking around while chopping, cooking, or cleaning before my joints start to get achy. However, when I am barefoot it only takes about 15 minutes. In interviews I have heard from Chris McDougall (the author of Born to Run) he "going barefoot" is always better, if you are running, walking, or just standing around. The argument is that your body knows how to adjust to avoid pain far better than whoever is making the shoe.
Obviously I don't really have much of a case against his point, but over the past two years while back at BYU running barefoot almost exclusively and I haven't felt it help my joints at all. In the past if I ran over 3 miles I would start to ache all over. Well, now when I run barefoot the same thing happens. I haven't been able to notice any health benefit from tossing my shoes. I really want to say that there are benefits because in a crazy way I feel that would add proof to Hayek and Taleb's arguements made in The Fatal Conceit and The Black Swan, by essentially showing that our bodies are so complicated that we can't understand the consequences of our own intervention and hence our "improvements" well only cause more damage. But, so far the only benefit I have seen has been that I haven't had to buy new running shoes for 4 years.