Wrist and elbow problems are more common, but shouldar issues can also occur, especially if you ned up moving alot of computer Chassis around or server boxes.
A couple things to check ergonomically. are your elbows properly supported by your chair when you type? if not, do you have to roll your shouldar at all forward to reach your keyboard? particularily your right shouldar? If you find that you have to adjust your shouldar position to type, you may want to consider looking into one of these keyboards: http://www.kinesis-ergo.com/
specifically the one where the keyboard segments split in half and can be positioned so your shouldar ball joint isn't rotated at all when you type. Also look into a full length keyboard tray wrist rest (you may need to make your own if you can't find an appropriate one)
You also may want to switch to a trackball, as some people mouse with their shoudar rather than just their lower arm, I personally can't stand the **** things, but they do help some people.
Chances are you will need to have the shouldar looked at by a doctor though, and surgery will be likely.