I am noticing that another exception to the Transform Input Shader when you try to adjust a shader setup that has been rendered grayscale and adjusted for masking.
The transform input will work on the raw merge shaders. (Actually it doesn't) Is this an exception to the transform input shader or an issue I am having?
The Merge Shader in v4.1 has a few different textures space modes for different scenarios. Some of them might be ignoring the texture coordinates (either by necessity or due to a bug). Perhaps a different mode will work for you.
Matt