I used to have pain like that and I had a medial branch nerve block and the pain went away and has not returned... I would check it out if I were you... hope you find relief soon.
I get that too, often actually, because I've had muscle problems since I was 12. If it's the same thing, then you have two options - firstly wait, because it does go away after a long and annoying while. Secondly (and much better) go to a Physio and tell them, they'll do a sweet deep tissue massage or trigger point therapy and do whatever they tell you to do (exercises, take it easy, or whatever) it should get better after that. The massage will probably hurt, but the more it hurts the better it wil lbe afterwards.
Basically it's a giant knot in your muscle. I'm guessing you have reduced range of motion if you try to learn your ear in the direction of your shoulder on one side?