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Have you had anyone look at your running technique or had someone video tape you running?
This will allow you to see exactly what you are doing.
Your body is able to buffer the fault (s) in your running technique for some time, but it sounds like at the 1 hour point you reach the point where your body can no longer buffer the fault(s) in running technique.
The pain you begin to experience at the 1 hour mark is your body’s way of letting you know that something is wrong.
The combination of uneven terrain and fault(s) with running technique are more than your body can buffer after the 1 hour mark.