It almost certainly sounds like you are holding your hands, arms or shoulders too tensely either when you run or at some other time. I used to get similar problems when I was going through a stressful patch with work. I was too tense all of the time, but it only really manafested itself when I ran.
Take a look at how you sit in the car - do you really grip the steering wheel or are you relaxed? Also how you sit at a computer, when in meetings, when talking to people, whan watching tv etc.
If the muscles are already tired and over worked then running might just be the final straw.
You may benefit from some upper body strtetches and strengthening exercises. Also a massage might alleviate the problem in the short term so that you can work on putting a more permanent solution in place without so much discomfort