I'm having some other shoulder issues to but your problem sounds like one I've always had.
I spent time in the Marine Corps, and obviously, used to run quite a bit. I always had shoulder pain on long runs but never bothered to deal with it since it wouldn't last past the run.
Now that I'm older, I pay more attention. I've had plantar faciitis to work through, as well as something runners call a 'calf heart attack' (repeated micro tears). I've been able to work through those by changing my running form.
In that line, I notice shoulder pain when I run distance and allow my shoulders a broad range of motion. It's a natural instince for me to shrug when I pump my arms. Try running, while paying attention to inadvertent shrugging and see if you do any better when trying not to shrug.
Hope that helps.
C
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