Multiple materials, one submesh - alpha problems

Hi there, I looked around to see if anyone else was having a problem like this but found a few things only tangentially related...

We've recently made the switch over to Unity 5 and I'm having some problems with adding more than one material to a mesh. Specifically, this is for adding customizable makeup to a character. In Unity 4, we were able to do this by increasing the size of the Materials array and putting the material for the makeup in the last slot in the array. The makeup material worked well with an alpha and a spec map, when we imported the asset bundle the makeup worked great. Moving over to Unity 5, everything seemed to work the same way. I ran the game from the editor, and the makeup worked perfectly. However...

When we made a build and ran the game from the exe file, the makeup alpha no longer worked. I couldn't for the life of me figure out why, when it worked perfectly in the editor. I ended up having to remove the spec map completely in order to keep the character's face from showing up a solid red. It seems like, for some reason, the spec map overrides the alpha on the albedo map. I'm using a standard specular material on Fade render mode. I really feel that we need the spec map to make the material look the way it's supposed to, but this is the only workaround I've found for it so far.

Has anyone else run into something similar?