I am not really sure. It looks like there is something going on with the material. If you are using a two sided material effect It has to know which direction is up and which is down in order to work properly.
In your plant modifiers do you have vector directional modifiers on all paths ? I usually put a vector directional modifier on every path to specify which direction will be treated as up (positive) and down (negative). If you don't you will sometimes get strange results on your later paths (leaves).
These black spots might be a result of normals facing the wrong direction on the leaves. This is just a guess. Maybe you could try a flat material and see if you still get strange results ? Is your leaf material a two sided material ?