My son (3) is having the same issue. there are times that he will poop in the potty but other times he poops in the pull ups. He's good about telling us though that he just pooped. With him there seems to be no rhyme or reason for when he goes in the potty vs. when he goes in the pull up. Like yours, he has no problem peeing in the potty and does like to stand for this. We resort to bribing at times - a tootsie pop for pooping in the potty, but that still isn't a cure all. I've talked with the daycare worker about this issue and she has suggested that we focus on this after the holidays when things return back to somewhat normal for him. I try to remember to let you know if and what works for him.
My son (2 1/2) and I are going through this too...he really really hates pooping in the potty. He has pooped in undies, and in his 'nightime undies' (Pull-Ups). Today, though, he DID poop in the potty and got to put a sticker on his chart...when he gets 6 stickers for poop he gets to go to the store to get a prize. He also got chocolate and we called Daddy at work to tell him. Making it a big deal if he ever does do it is seeming to help.
Maybe try to recognize his need to poop--my son will toot for a bit and between lunch and nap is when he tries to go--so if I can rush him to the potty, and he goes, then we have the big deal celebration...it's a start. Good luck!
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