The answer is likely lie in the gait analysis. I imagine that you had this done in a running shoe shop, and probably they put you in "motion control" or "support" shoes? Is that the case?
The theory behind this is that if you over pronate (i.e. roll your foot inwards on landing and push off the inside edge of your foot), shoes that are built up on the inside can help stabilise your foot and stop you from doing this. The idea is that this change in your gait will help prevent injuries that can be caused by over pronation.
The reality is that, by significantly changing the bio-mechanics of your gait, what the shoes actually do is radically change the way your foot works, causing immediate problems in the lower leg - most commonly shin splints or inflammation of the small ligaments in the lower leg or foot. BAD NEWS! Actually, if you are a pronator, the chances of this causing pain is far smaller than the problems caused by attempting to "fix" it.
The good news is that there is a very good chance that if you ditch the (sadly expensive) shoes, and get yourself into a pair of basic, minimal -style shoe (I like the Adidas range - Adizero or Boston; Nike Free; Brooks Pure, but all the companies do them). Start slowly, run short distances in them at first and concentrate on your form. Think of running light on your forefoot, lift your knees, relax your topline and take short, high steps.
You will be amazed how quickly you will be running pain free.
RANT ALERT: Bloody shoe shops and bloody gait analysis. There are a few people whose over or under pronation genuinely does cause problems, but they usually PRESENT with problems first. If you run pain free and pronate, forcing you to run in a different way is bound to cause pain! So why do the shoe shops do it? Because it is a good money spinner. They can sell more expensive shoes. It is "pseudo-scientific". But sadly it really does cause problems.
Good luck!