I think I've encountered a sort of very specific bug that I'm not sure how to get around.
If you make an object - any sort of object - that has the ink effect "subtract", and then set the layer that it's on to any ink effect (HWA needs to be on for this, of course), then the object will show up as a single blank color, ignoring anything else about the object beyond transparency. This ONLY happens with the "subtract" effect, and ONLY when the layer it's on has a non-normal effect applied to it.
Observe...
Notice on the bottom how the gradient becomes nothing more than a hole to the layer below?
I'm fairly new to using layers for effects, so I'm kinda stumped here. Does anyone know why this would be happening, or have a solution or workaround to it?
It looks like the shader stops using the gradient information as an alpha channel, and is simply applying 0.0 throughout. I don't know why there'd be a cutout; maybe you found a specific problem with the way MMF's layer shaders interact with objects shaders? Or maybe it's simply something in the code of that specific shader effect.
You could try finding another shader that does the same as the subtract shader and see if that does what you want. Or maybe you could ask someone that knows HLSL? If you post it on CT's forum, I'm sure someone will help out.