Prefabbed leaves dissapear or scale weird on Unity tree

after making a nice looking tree with the unity editor I put it into a prefab so I could use my own LOD's for it and place them manually around my scene, however some instances of the tree will have no leaves on them or the leaves will be shrunk down greatly and skewed. The scale values are all uniform, I did find that a tree using billboarded leaves that has non-uniform scale would encounter the problem described above, however even after fixing this it is still casuing problems. Ideas?