Several ideas here...

1) is the consistancy of the poop dry and hard at all or have alot of hair packed in it? Reason I ask is that Jack, my megacolon cat, did that whenever the hair got too packed in, and again several times just before he was diagnosed megacolon. If the poop your cat leaves is hard, dry, and/or packed with hair a trip to the vet may be in order.

2) are you using an enzyme pet odor cleaner on the spots? If they smell anything the cat will keep using the spot.

3) is the litterbox large enough?

4) is the other cat bothering this one when he's in the box?

5) are both cats neutered?

Other than that, I don't have much for suggestions. At least be glad it's poop and not urine as that is much harder to clean up.

Good luck.