Placing Custom Trees with Unity Terrain only Places the Bottom Part of the Trees

I have a tree in Unity that when I place into the scene by itself works perfectly fine as you can see:

However when I use the terrain system to place the tree, using the same prefab, it only shows the bottom part of the tree:

The tree that is working properly is the one that I placed by hand and not using the terrain system. I can't seem to figure out the problem, and I think it is something to do with the terrain system because if it works when I place it by hand it should work when I place it using the terrain, right? I'm also not using the Nature shaders on my tree materials because it screws up the trees lighting, but when I do use those shaders it still only places the bottom part of the tree.

Any suggestions?