I began taking Accutane in September. I started out 40mg a day. The next month I went up to 30mg 2 times a day along with 10mg of Prednisone a day. I am 16 and I am an expierenced xc and track and field runner.
I am half way through my second month and the only side effect truly affecting me is the joint pain.
I went for a run today and I could not believe how bad my knees and lower back hurt. Never in my life have I stopped a run short due to pain, but this was unbearable. I could barely move my legs it was so bad. I really do not want Accutane to effect my joints long-term. If you guys could PLEASE give me some input and advice I what I should do. I am thinking I might stop taking Accutane because I do not believe clear skin is worth my running career. If anyone has experienced these same effects, please give me some insight on the outcome of your decision! 
From the information booklet: "Accutane can affect you if you do alot of physical training or sport. You may experience muscle fatigue which can lead to poor performance. You should also try to avoid contact sports while you are taking Accutane. If you are training for an upcoming event or playing a seasonal sport you may wish to delay your Accutane treatment until a more convenient time."
I think its rare for joint pain to be long-term or permanent. I'm nearing the end of my 3rd month and I still experience increased lower back pain and muscle fatigue, which is a problem because I swim a lot. It doesn't bother me that much considering Accutane is saving my skin. But in your case, it sounds really bad, so you should definitely ask your derm on your next appointment.
Oh, and try taking lots of fish oil pills. They're cheap. I started taking 6 pills a day a couple of weeks ago and they helped alleviate some of my back pain.