If you think you have a strained bicep, you should see a doctor. If you think you have a "not that good" shoulder, you should go see a doctor. He'll have better answers than we will.
On the other hand, you could just have shitty mechanics. If this is the case, and you take throwing seriously, taking a few lessons from a pitching/shooting (basketball) coach would probably be a good idea.
I have had a similar problem to this and had to go to physical therapy for it for a few weeks. They really emphasized stretching and making sure you were including just as much back exercises, such as rows.
A) Stretching anterior chain of your shoulder girdl and internal rotators (pecs, lats, anterior shoulders) B) strenthening external rotators (teres minor, infraspinatus, posterior delts) C) Stabilising shoulder blades - strenthening rhomboideus and low/mid parts of trapesius - loads of various rows and vertical shrugs and others D) See someones who knows and can have a look at your throwing mechanics (you might be doing something wrong in this department) E) - this should be first really - EASE OFF your throwing for a while - get your legs and hips as well as you weak points when you rehab your shoulder. F) See your doc or GOOD THYSIO/ART therapist
I have a similar problem due to a torn labrum. I can't throw anything without pain. But I can toss a frisbee without a problem (different movement). I also have to watch what exercises I use to avoid pain.
What you're describing is exactly the pain that I was having during last football season when I would throw a ball around. The school athletic trainer told me to do this stretch where you externally rotate your arm, and to do external rotations in the weight room. It seems to have improved a lot since then.