I had EXACTLY this with my eldest and it drove me nuts. He was fine with the loo and still had nappies for bed. He would poo in the nappy the second I put it on him! The only advice I can give is to carry on the way you are without taking a backwards step. My Health Visitor told me that as long as he wasn't pooing his pants, or pooing somewhere inappropriate, it meant he had the control of his bowel. The physical side is the bit to worry about and your son obviously has the control. Mentally, it's a whole different thing. They have to CHOOSE to do it on the loo, and that is the bit that you can't help with. When they've made that decision, they don't go back! HV told me it was like a switch being turned to 'on' - they didn't want to turn it back to 'off' again. In the end, at nearly 3, my son decided to do it on the loo suddenly. Hand on heart, the problem disappeared overnight. 2 days later we were in Sainsbury's and he said he needed to poo. Normally that would have been a total disaster, but this time, I took him to the loo and he went quite easily, like he'd done it there 100's of times. It was at that exact moment, seeing him on a strange loo to poo, that I realised HV had been spot-on!!
Don't get cross with him, keep asking if he'd like to try the loo, make it easy for him to go the way he chooses to go for now, and one day he'll make a different choice. I REALLY feel for you - it drove me mad but all that was a waste of effort!! GOOD LUCK - don't let it get you down :o) xx