It's hard for people to tell without a video of you deadlifting. Dayna, I'm very new to all of this myself. Could you be using your shoulders/traps to help pull the weight? Your arms should just hang there. I know that when I first started deadlifting I brought my arms up a bit during lockout. Until someone watched me and told me I was doing it, I never realized.
Or it just could be as NW said: this is a new move for you. I felt mine in my lower back more than anything when I started.
Whats wrong with shrugging on a deadlift? Personally I think it just incorporates more muscle for more of a compound excercise. I know CCJ does it.
And by the way, I would say that is why your shoulders hurt. They just have to get used to it. Im like everyone else, after my first dead lift, my tongue was even sore.