I don't have a solution for you, but I have/had a similar issue. I was coughing horribly hard due to flareup and my rib/back became sore. Then, one day when coughing I heard/felt a pop and had excrutiating pain to where I couldn't walk, bend, etc. My husband had to practically carry me to the car. Anyway, I either cracked a rib or popped one out of place. They couldn't tell though since I was pregnant and they didn't want to xray. Anyway, I got pain meds and after about two weeks the severe pain eventually faded. I still have rib/back soreness upon waking and when coughing, and it's been 3 months.
I'm not telling this to scare you, because hopefully, if your son is getting over his flareup it won't turn into anything. I just wrote about this topic in the adult section about a week ago and only got a reply from someone who'd played rugby and injured themselves. He said it could be the intercostal muscles between the ribs and that they were hard to put back into place.
Anyhow, I told my CF doc at my visit last Thursday that I was still sore and he had no response. I don't know if there's nothing they can do or if I'm talking to the wrong kind of doctor. <img src="i/expressions/face-icon-small-wink.gif" border="0"> I am considering trying to find a type of doctor who may help with this, although I'm not sure if it will lead to any results. If it does, I will post about it.
Well, I hope your son feels better soon. <img src="i/expressions/face-icon-small-smile.gif" border="0">