I used to be a long distance runner. I ran in high school track but didn't get serious until I joined the Navy and started running to get a high score on my Physical Readiness Test. My feet and ankles started to bother me after I started to train for my first marathon. I went to see my doc and he said that I had tiny hairline fractures in my foot and that is what was causing my pain. I didn't like it, but he ordered me to stop running for a few weeks.
I would get hairline fractures and they would heal and then I would get them again ... and they would heal. Maybe you should check with your doc?
TREKSTRONG