What would cause the background to seep through the leaves? I've attached the two materials of the trees.
I do not see any vegetation shaders being used in these material files - does that mean you are hand placing these tree models into your scene and not using the vegetation tool? If you are using the vegetation tool available in the Terrain tool options, then I would recommend using vegetation shaders as well or you will get weird artifacts/shadows.
Also, zsort on the leaves' material is enabled - that will affects the shadows that occur on the leaves and maybe related to what you are seeing