Hi Ulco,
The "shader" input is only called if the Transform Merge Shader is enabled. If it's disabled, it will simply act as a pass-through for the main input (just like every shader in Terragen). The shaders that you want to transform are not connected through the main input (nor should they be with this shader), so there's nothing to pass through.
Perhaps you should be using the Transform Input Shader instead? Then you can enable/disable it to enable/disable the transform effect.
Matt