Debbie my son (SWCAH) has suffered headaches all his life!  I was originally told they had nothing to do with CAH, turned out he had a sinus problem, they eventually sorted that, however the headaches continued.  Changed endo’s and was told headaches can occur with CAH when there is over or under treatment.  It could be that your son runs short of cortisol in the afternoon, is he on 3 doses a day or two?  It could also be that he gets a little dehydrated which can also cause headaches.  We eventually found the problem with my son by doing a 24 hour cortisol and 17 OHP profile.  It seems such a common problem for people who have CAH - I am hoping one day an endo will take a real interest in the problem! Good luck.