I'm sure a few people here have had some experience with weight training related shoulder injuries... My shoulder's been somewhat screwed since my swimming days but this might be a little more serious.
On chest days, I can feel pain in the back half of the left shoulder usually after the third pressing excercise.
And on a back day, I get this popping sensation (not painful though) in the same shoulder when I'm doing pull-ups. It feels a lot like cracking your knuckles.. only I don't know if your shoulders are supposed to do that .
I have the same problem minus the popping, especially doing incline and bench press. I think its mostly a positioning problem because I only get it in my left shoulder as well. My conclusion on it was that i might have been off center and and just strained it too much.
I now do DB and i feel a lot better. I still have a little twinge with it, but not that bad.