I'm trying to learn the process of using multi-tiles and advanced texture/rendering workflows, so I created a simple beveled cube and placed each side on a separate tile (MARI 'patches') and would like to start stacking maps on it.

My goal is to have a base diffuse layer (metallic) with a small bit of surface rust, so I've added a spec map to dial back the rusty spots. I've been successful with getting both of these to play nice with each other using a Blinn. I haven't figured out how to get the spec map to work with a Mia-X material though.
My first problem though is that the top map (with a heavier amount of scaly rust) is not abiding. It's RGBA but the alpha keeps showing up black.

I've looked at the maps that MARI has generated and can see the alpha in Photoshop and when it's plugged into a simple Lambert, but the moment the texture is put into a Layered Texture (using the same Lambert) it goes black.

I've also messed with the different blend modes in the Layered Texture node and have also tried to plug the RGBA files into the Alpha slot of the texture layers but nothing is working.

Help!