I'm not a PT just a frequent patient! My experience has been that these types of injuries can hang around a long time unless you get good treatment. It doesn't sound like your orthopedist has really diagnosed the problem which makes it harder to treat. All the MRI is telling you is that there is no physical sign of the problem but you can still have trigger points or strains or inflammation. I would get a good orthopedist to look at it, then get a good PT to work with you. Also consider ART (active release therapy).
Again, left untreated, these things can go on. My theory on this is that the shoulder muscles and tendons are layered and don't get as much circulation as other muscles so the healing process is slower.
In any case, please be more specific about the pain and perhaps I or one of the PTs can help.