I had that problem several years ago and it ended up being my shoes. They were too old, too broken down. Another one of my friends had the same problem but she had just gotten new shoes. Turns out they weren't right for her arch type. There are three basic kinds of running shoes - cushioned, stability, and motion control. She was using cushioned when she should have been using motion control. Roadrunnersports.com can help you find out which running shoes are best for you depending on your arch type and running mechanics. It's under the "Shopping Tools" menu choice and then under "Shoe Dog".
That's the extent of my knowledge. Hopefully it will be that simple for you and can easily be corrected. Good luck to you!
~ Wendi
Do something EVERYDAY that scares you just a little.
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If you're doing something you love, you are the luckiest person in the world.