It sounds to me like a neural tension issue ... try this stretch variation and see if it helps ... if it helps a little, but doesn't completely relieve it, I can give you a "stronger" version.
Lie on your back and bring the involved leg up toward your chest, lacing your fingers together behind the knee. Let your hip relax so that your arms are generally straight (your hip will be bent about 90 degrees).
Extend your lower leg up toward the ceiling (straightening your knee as much as you are able). Now hold it there as you slowly bend and flex your ankle (dorsiflex and plantarflex). It will probably feel different during dorsiflexion than plantarflexion (degree of stretch). Perform for 30 seconds each leg, twice.
Do before your run and see if it impacts the onset. If you can, when it comes on, try this stretch and see if it helps. (not great if running in the woods or on the road, but doable on a treadmill).
Let me know how it goes ...
