I have a son in middle school.  We have had a rough year with him also.  He is going through the phase where he is very concerned about being different and fitting in.  Midddle school is tough enough, even when you are healthy.  My son has gone to the nurse repeatedly this year for stomach related issues.  I went as far as to take him to a Gastroenterologist.  They performed an Endoscopy and found nothing.  He was diagnosed with Irritable Bowel Syndrome.   This was stress related.  He was becoming physically ill every day in math.  Pulling him out of school wasn’t the answer.  I felt that this was the time to teach him how to stand up and deal with his stresses appropriately.  

We found out a few months ago that when we moved into this school disctrict last year, they had placed our son in the advanced class without our knowledge.  At a point of desperation, we considered moving him to a lower class.  During the meeting we discussed accountability and I found out believe it or not that some of my son’s teachers were allowing him to sit in class and do nothing all day.  For some crazy reason, they didn’t think they could say anything to him. I told all his teachers that I wanted him held accountable.  I was tired of staying up till 10pm every night pushing him to do the volumes of homework he was bringing home.  Do you know that from this point he did a complete 180 and has done wonderful.  I guess my point to this long and drawn out story is that we need to support our kids, but they also need to understand accountability.  Kids with CAH need to learn how to deal with the stresses of everyday life.  What will they do as adults if we don’t let them learn these skills?  I am one of the most overprotective mothers out there and this is very difficult for me.  Learn from my mistakes.

The absences you are talking about sound very excessive to me.  As a matter of fact with all the problems my son has had this year he has only missed 7 days.  In the past, hospitalizations would pull him out of school for up to a week.  As stated in some of the other posts, it sounds as though there may be some emotional issues to deal with.  I know there are many more emotional issues for girls than for boys.  Counseling might be the best place to start.