Issue with feature generation

I'm having an issue with generating features. When I generate a feature using the /place command or try to generate a tree using the new sapling plant type, some of the blocks are missing until I place another block in its place. When I place another block, the intended block reappears where it was supposed to be. On the topic of trees, not only are the blocks missing, the trees are off center when I grow it from a sapling. Also, when the trees spawn naturally, they are either floating or missing blocks. For regular features, such as a custom monster room/dungeon, they don't spawn naturally for some reason. Is there any way to fix this?