I started having problems
I started having problems with my AT about two years ago, back before I discovered barefoot running. I had taken a several-month-long break from running to get my thesis finished, and when I started back up again I was over-anxious to get back in shape and overdid it with back-to-back intervall days and the like. I finally went to the doctor when pain turned into a visable bump at the base of the tendon on the heel. X-rays showed it wasn't a bone spur, and since the doctor couldn't really figure out exactly what it was, he perscribed inlays with a raised heel. After about a month the pain was gone, but after about six months I started noticing the first signs of PF, which I can only assume was a wonderful side-effect of the strange inlays.
A year ago I started barefoot running, and within two months all signs of the oncoming PF were gone and have stayed gone. The AT has been another issue, however. All was well until this last June when I ran a 12k race on hilly terrain after running almost exclusively on flat terrain for the last few years. A few weeks after the race I was in San Francisco on vacation, so of course there were only hills to run on. Then a few more runs with the Oregon BRS Chapter in the hills of Forrest Park in Portland and my AT was back to its old self. In July I finally broke off my marathon training
and cut mileage way back, and I've just about got things back under control.
Everybody (every body) is different, but for me personally, I can say with confidence:
1) Barefoot running didn't make my AT worse. Over-training did.
2) Barefoot running has taught me to listen more closely to my body, which I believe is the greatest key to preventing injury.