Perhaps its just the muscles in your shoulders building, Especially if you are not well exercised in the upper body area. What do you ride? DH, DJ, FR.

I get shoulder pain but thats due to a stack where I dislocated my shoulder and fubbarred all my ligaments. Perhaps its worth popping to your local chiropractors they've worked wonders on my shoulder and neck.

Either way it'll sort its self out the more you ride i expect unless you have a genuine injury that you are agitating which is where chiro comes in.

cheers

Try doing/increasing weights, and push ups. I had a similar thing when i started. Building my upper body strength definately helped minimise the recovery period after riding for me