Debbie,
Yes the litter boxes are cleaned very often, I make sure of it because of this problem. However, I think I will thoroughly disinfect the carpet (thanks Burt). We moved here from Cali 14 months ago and he never did it there at all...then we got the female spayed here in NY and she became more loveable and that's when this started...maybe he's feeling left out or something as the female now gets petted and cuddled as much as he used to...now he has to share.
Thanks for all the thoughts