Do you have black toes? Could be that your shoes are just a tad smaller and your toes hammer against the shoe as you run. Or, you are not properly hydrated.
Just heard on an interesting podcast that when the body is not hydrated well, all the available water is channeled to the core functions of the body away from the cappilaries at the end of your digits....
So, if you have black toes, not only change your shoes but start drinking more