Hello,
As I am new to Maya I hope the following description of a problem I am having is coherent.

I have a scene (Maya 2012) which contains an object, the object has mib_illum_phong and misss_physical shaders applied to it. When rendered with MR it looks good in the Render View window and upon saving a layered PSD I get a PSD file with an appropriate alpha mask. So far so good.

Changing the the mib_illum_phong to a shadingMap/rampShader (connected to the misss_physical shader) followed by rendering also gives a nice image in the Render View window. However, when saving the image (in a variety of formats) the alpha channel has no mask and is completely black/transparent. When loaded into PS, the 5Mb file only shows the transparent alpha channel..

In both cases MR render settings: 'Alpha channel (Mask)', and 'Pass Custom Alpha Channel' are checked; and Image format: Maya IFF is selected.

Any ideas why my object no longer 'punches a hole' in the alpha when using the color ramp?
Does this happen because the rampShader is a Maya shader and not a MR shader?