I have ran a support group for families living with reflux since April 2002. In that time, I have never heard anyone else complain of shoulder pains.
One thing with reflux is, if you are having an episode, perhaps you hold yourself to control the pain and that brings on the ache etc or it could be that you have another condition, whereas reflux is a symptom rather than the initial diagnosis.
For example, hypermobility, fibromyalgia fall into this catergory, along with CF, Down's syndrome or any other condition that lowers the muscle tone.
I would suggest getting a doctors opinion just in case.