Is it during the breathing action of cervical rotation or during the exhalation stroke with the cervical spine in relative 'neutral' ? I would deffinatley raise an eyebrow in the general direction of the Cervicothoracic junction. If breatstroke (with minimal cervical rotation) is pain free then the that is a good clue. Try checking cervical rotation in thoracic neutral (watch for cheats) and at variou ranges of thoracic rotation (better still, as suggested, in the patients painfull position) and look for differences.

I would deffinately also be looking at scapula stability and control through range and in functional position. Use repeated movements and sustained positions or wieghts (even 1 kilo will do) during range to fully explore this - one quick rep might not do it!

Over activity in scapulothoracic muscles could be rotating the thx or CTJ under loading and upsetting biomechanics.

Swimmers regularly throw up the most complex and confusing cases especially as its hard to assess then fully functionally on dry land!!

I hope this gives you some ideas of things to check. I would say practice checking these things on 'normals' so any descrepancies will be easier to identify.

Chocks Away!!!