Same "old hat" here with a shoulder injury I've been dealing with for what seems like 6 months now.
Shoulder injuries certainly seem to be the norm, and from what I gather the good ol' flat bench seems to be the main culprit.
Not sure how I hurt mine, probably from flat dumbbell benching.
Regardless Dante's post "How to cure shoulder problems" helped me out a lot.
That coupled with some Icyhot afterward fixed me up probably as good it's gonna get sans a Doctor.
Using DC's rehab protocol I also avoided any kind of flat bench work, and still do. I noticed the only time I would get a nag in it is if I would do any kind of flat benching so I resolved I would just switch to incline.
Rippetoe has an interesting philosophy on injuries, stating that, "there are those that you can train through, and those that you have to train around."
I agree with him and I swithced to incline work and weighted dips for my chest.
Just listen to your body, if something is causing you the kind of pain you know that could escalate into something further, drop it, and train around it.