My oldest DS was the same way. At two he'd use the potty without fail as long as he was "nudey budey". In pants of any type (underware, pullup, diaper) he could care less. It wasn't that he didn't know, it's that we waited so long past his window of interest (I'm convinced) that he learned not to care about using the potty. Well, at home I did let me run around naked from the waiste down as long as we didn't have company to get him used to not going in his pants. And when he went in the pull up (wish they had the feel wet kind then), we didn't make a big deal out of it--just changed him. Well, after about 6 months of this, no more accidents. One day I said "we're out of pull ups and Daddy bought the wrong size" (True) and "you'll just have to wear underwear and not have an accident". He said OK. And never had an accident again. Even woke up at 11 pm that night to use the toilet. The other boys I started training sooner & they were all trained by 2 years (part of my window of opportunity theory--can't start too early, but don't wait too long or it will be long).
OK, so my advice is: Let him run around with nothing on the lower half and unless you have company or are out and about. Use the feel wet type (like underware without the mess for you) of pull ups when people are over and when you go places. Then when your DS is ready to move on (no pull up accidents), then pull out the underware. Don't make any kind of big deal his being naked or having accidents and it will probably all fall into place sooner than you think.