Maybe he is lonely?
I had a very simular situation with my cat Tommy. Are you away from him often and do you give him tonnes of affection. I ask because the man who had Tommy before me, wasn't home a lot and even when he was home he did not pay too much attention to Tommy. Tom was already litter trained when he got him, but Tom pooped everywhere BUT the litter box. When Tommy came to me I showed him the litter box and didn't have the slightest problem. He is the neediest cat I have ever owned, he has never been content unless he is cuddled by my side. During the summer I stayed at a friends house while they were away and even though I stopped in at home every day for about half an hour or so I noticed that Tommy was pooping anywhere But in the litterbox. When I returned home to stay he was fine again and I have not had a problem since.Do you think your problem may be simular?