OUCH! Hopefully it's not the saddle!
But you may want to have a good bike fitter look at your position. One of my cleats was positioned wrong and I had no clue. I was having terrible knee pain. He moved my cleat and I was golden. If you can't find one out there I can try to hook you up w/ Robin Oswald from the trinewbies forum. She lives in SLO and is a pro triathlete/coach. I don't know what she knows about bike fitting, but she could probably help you- or know someone who could...
Good luck! I hate bike related pain! I want to get on my bike and enjoy the ride!