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What are you doing to strengthen your feet?
Are you working to resolve your pronation?
Have you had anyone look at your running technique or video tape you while running?
You may have fault(s) within your running technique that need attention.
Are your knees still a problem?
This definitely could be a running technique issue.
What is your ankle mobility like?
Do you work on your ankle mobility before running or jump rope?
There are some solid episodes that address ankle mobility.
A few to start with