It's going to be something that you should be able to sort out with the aid of a good podiatrist / running shop.
Many running problems can be a result of over structured and engineered shoes. Much of the current thinking is devoted to loosing structure and reducing heel lift to promote a natural mid/forefoot strike. This encourages the bodies own biomechanical structures to operate correctly, absorbing shock and strengthening bones and soft tissues in the foot and lower leg especially.
I had a similar issue with my knees after 6 - 8 years. I wrote a little piece for my local running shop giving my story. It's pasted below if anyone's interested in reading it.
Evolution to Minimalist and Barefoot running
Firstly, just a quick note about me, just to put your mind at rest. I am a self employed electrician and Solar Photovoltaic energy installer, not a bearded hippy barefoot evangelist, but someone who has come to understand and enjoy the benefits of minimalist style running. Here is my story.
Up until about 5 years ago, I didn’t ‘run’. Until then, I had concentrated on mountain biking, competing in the Polaris Challenges and generally riding in and around the peak district. Also supplemented with general fitness and strength training, courtesy of British Military Fitness (BMF). A friend suggested that the Tough Guy in Wolverhampton might appeal. It did. But, running was my Achilles heel. I just didn’t enjoy anything about it. It was time to knuckle down and get on with running. Without which, I’d probably end up with hypothermia and fail at the Tough Guy.
So, off with the cleats and on with the running shoes. I invested in some Inov-8 Mudclaw 330s for the TG and BMF. Great shoes that work, and do what they say on the tin.
After a few weeks, of aches, discomfort and sore legs, imagine my surprise and the realisation that something had changed. I was both enjoying and looking forward to running. This continued, to the point were I would get round the Tough Guy. Then, disaster. A torn calf the weekend before. TG postponed for a year. Enforced rest followed, and eventually, the legs would work again. Once again, I went through the discomfort threshold and began running again.
I discovered running off road and my enjoyment of running continued to grow. But, at a distance of 6 - 8 miles, my knees would start clicking and giving me a lot of discomfort. Not pain exactly, but enough to slow running down to a miserable trot or hobble.
I came to realise that the problem was the shoes I’d been using. They were name brand consumer shoes, purchased from a well known sports supermarket outlet, chosen because the felt ‘right’ in the shop. So, the decision was made to go to a proper running shop and get some shoes that would sort the problem out. After an hour or two of trying shoes on, running away with two pairs of new running shoes. A pair of New Balance 759s for the road, and New Balance 840s for trail running.
I walked away happy that distance would be no longer a problem. It was immediately evident that both pairs of shoes were a great improvement on those that had been retired. But, the knee issue had not been vanquished, merely delayed by an additional couple of miles.
At around this time, I had heard an interview on the radio with Christopher McDougall, talking about barefoot running, the Tarahumara, injuries and his book, Born to Run. I was intrigued and promptly went to Waterstones to acquire a copy. It wasn’t in stock, but arrive the next day.
The book was spellbinding. A great tale of exploration and enlightenment, but most of all inspiring. If you haven’t read it, do so! The next day I decided to give this barefoot thing a go. The immediately surprising thing was how little it hurt. I was fully prepared for lots of discomfort but it wasn’t there. Yes, I could feel the ground and different textures but definitely not pain. I think I ran a couple of miles and it felt good. Very good.
However, the next day, my Achilles and calf muscles were very sore. I was aware that this could happen, and that learning to run barefoot was going to put additional stress and strain on feet and lower legs especially. With hindsight, I think I did too much too soon, and would have benefited from a more gradual progression to full barefooting. I am sure that my legs suffered less as a result of sailing, in particular a 49er that requires a great deal of active balancing on the balls of the feet. The result being stronger ankles and ligaments than may otherwise have been the case. This coupled with BMF and the exercises and drills made my reasonably rapid transition to natural style running quite swift. Nevertheless, the aches and pains lasted for a couple of months, off and on. Not wanting to risk another injury I didn’t barefoot when my legs were feeling very stressed.
Whilst making the transition to barefooting, I read websites and forums and watched various online videos. One of the results was making some huaraches following the plans on Barefoot Ted’s website. Why? Because I had discovered that running on ‘improved’ surfaces, crushed rock for example or country roads surfaced in tar and chipped stone was desperately unpleasant to run on. The huaraches provided enough protection with their 5mm sole to allow comfortable running virtually barefoot.
Throughout all of my barefooting to date, I have also run and trained in shoes.
I quickly realised that my running style had change completely, even when shod. My favourite shoes became the New Balance 840. Now I was able to comfortably run 20 – 25 miles without any issues with knees, feet or any other joint.
Moving on, the story continues with another injury. Caused wearing shoes, but not I hasten to add, cause by shoes. Running one Sunday evening in December, I went over badly on my ankle on the ice. This coupled with additional injuries cause as a result of running again to soon caused a break of about 3 months.
During the enforced rest, I was luck enough to visit a discussion hosted by Accelerate at the Sheffield Action Film Festival, title Minimalist Running. Representatives from shoe manufacturers were in attendance, together with a podiatrist and an athlete who runs barefoot. Without going to great lengths to explain, my conclusion was that the footwear manufacturers were working towards the minimalist idea, but having to add support and structure to many of their shoes in order to justify their research and marketability of their product. However, one of the shoes on display made a very strong impression. The New Balance Minimus Trail felt very similar to the huaraches that I’d made the previous year. Sadly however, there were 2 samples, both left feet and both the wrong size. The shoes were due to be released later in the year so I’d just have to wait.
Since getting my pair of the minimus, they have been the only shoe that I’ve worn, road or trail. Having said that, I am doing more barefoot running than ever, and enjoying it more that ever. Enjoy, that’s the important word. Minimalist running is so enjoyable. It is a very relaxing way to run and travel. I would certainly recommend that you give it a try. I realise that the idea of padding along on the roads fills many with trepidation and fear of standing on glass or stones, but in reality, this doesn’t happen. Eye and foot co-ordination seem to do a pretty good job of avoidance. I do however suggest that you get some pointers on how to do it, find a smooth piece of tarmac, not grass, and give it a try. You may be pleasantly surprised.