could be loads of things!

the fact it doesnt bother him swimming or throwing is good.

can you describe where exactly the pain comes on.

does the pain come on instantly when he starts to run or does it take a time?

any other activities bring on this pain?

how is his posture?

is there a tender spot to touch that recreates the pain?

is the pain on his dominant side? (ie throwing hand)

its possible that there may be some muscle imbalance problems around the arm and shoulder/blade.