It might have something to do with shoe fit as well. Sheldon Brown (Google him) and lots of others on the internet will give you advice.

I would also suggest you try some inserts. I have Superfeet from REI (you can get them other places as well - on the internet too). I took out the original inserts that came with my shoes and put in these. Work just fine. These will give you arch support as well as change the position of your feet in the shoes. You might try these in your running shoes as well.