This was fixed in a later version of Maya, but I believe your problem is this: create a new shader shader Open ShaderFX inside shaderfx graph window: enable Settings / advanced mode enable Settings / Override system nodes enable Settings / Show Node ID drop down a "shadow map" node Go inside this group node by clicking on…
@CreativeSheep: It depends on what you want. Dx11 AutodeskUberShader gets you going very quick; artist friendly. DX11 writing custom shader: hard if you don't know any shader coding. ShaderFX is in-between. Quicker/Easier then writing shaders by hand for many people, but not as easy as the Uber Shader.
I should say that you can do this change in a empty Maya scene or the one you are working in. Since you are overriding the Shadow Map node in the end, this fix will apply to all scenes (if this is indeed the problem)