Pain and the mechanisms of pain are still a large mystery to experts. Even low intensity stimulation like a massage can be interpreted by the nervous system as painful instead of pleasurable.
If it seems okay at the time but causes painful symptoms later, then there may be some hyperexcitability on the part of the spinal cord. The nerves in the skin and muscles send messages to the brain via the spinal cord. If for some reason, the nervous system is over reacting, then normal, soothing touch can be interpreted as painful or noxious.
Studies of chronic whiplash patients show that this concept of nervous system hyperexcitability may very well explain some of their long-term symptoms. Even after the soft tissues in the neck are healed and there is no tissue damage observed, changes in the nervous system can persist.
Be sure and let your massage therapist know of this reaction. He may have some ways to influence or moderate the nervous system’s response to the treatment.