does sound a bit odd - reduction of kayaking, and now pain in both shoulders? Pain with ADL's and light activity?

Consider what the others have written e.g humeral head position, Cervical spine; but also look at what he's doing on a day to day basis - there must be something he is doing - bilaterally (i would guess) that is irritating him. Is it possible that the exercises you have given him are the source of the irritation?

A lot of athletes are very driven and I find sometimes do not get the whole concept of exercise that does not cause pain (esp if their livelihood depends on it) Does he tend to overdo exercises (through pain etc) - thinking that if it's sore it will get me better faster? Could that be the reason his shoulders are sore? Has he been doing the Wikipedia reference-linkrotator cuff strengthening etc on both sides? (that would possibly indicate the reason pain has appeared bilaterally) have you got him strengthening flexion/lifting weights/bench press? (i find that they can irritate the anterior structures of the shoulder)

I found manual release to the posterior capsule one of the most effective treatments for shoulders in general.

Cheers