I had exactly this pain, unfortunately I can't recap the explaination I got from my physical therapist, but essentially it was an inbalance issue.
Try this, keep your arms straight, hands facing eachother, about 20 cm appart, as low as possible, i.e. below your waist, then raise them slowly in front of you, arms straight, until hey are directly above your head. Any pain?
If so, do the same thing, but hold a rope or something stretchy between your hands, palms still facing eachother and keep the rope stretched out, then do the same movement. If this is pain-free and the former wasn't you have an issue with keeping your shoulders down in certain movements.
The exercises I got to do was external and internal rotations like here: http://www.bodybuilding.com/fun/criticalbench24.htm
And the same rope-movement, 2 sets of 15, each day, with enough "pull" to make you tired in 15 reps, ideally you have something stretchy because it'll activate your muscles more.