I think i might know the answer. So when you make a new bukkit world, there seems to always be chunk issues like that where you have square cliff sides, etc. I think you might just have to try and create a new world. If you already did that, then I'm not exactly sure how to help you :/ But I hoped this helped, because it also helped to me! So overall i think its a problem with bukkit, because I've experienced this before.
