Many people have that problem when switching from the too fixed (in-line) up and down motion on the Smith. The Smith does not allow the full natural muscle action of the "S" curve on so many exercises. Overhead presses, BP's, up-right rows & squats can fall into this group of exercises. Making matters worse, trainee's try starting with the same or near amount of weight on a regular BB. Using a free weight (BB) requires a different strength/body mechanic pattern to be learned. If not taken slowly than joint & tendon discomfort or injury could develop. As with the example of KingCol's.
Nothing wrong with the Smith, lots of guy's use one and get good results. Just that a little understanding of the limits when switching over to free weights may be needed. And the negative influence it can have on some people. But overall, I do not believe any serious max weight should be used on the Smith at any time. Just because of that too fixed position that is required.
That shoulder pain could be a number of things. Inflamed nerve, joint,tendon, muscle, etc. Take a couple of weeks away from direct training on presses, even benches and inclines. Only exception would be dips for the chest. That may not cause any undo stress on your delt/shoulder structure. Because, with dips, you are pressing down and along side the body rather than up and away from the body. Good Luck.