Do you stretch before you run?

You might try a knee and ankle rotation to help loosen and strenghten the ankles. It could be you just aren't stretching them out and preparing them for the run.

Bend your knees, place your hands on your knee, place your feet together, and rotate your knees and ankles. Rotate clockwise, then counter clockwise.

You also might want to see a sports doctor to see if there is any physical problem with your ankles.