Thanks nomuse, I'll try that.  On my partial mats there are lines referencing difuse/specular textures that upon inspection where left there when I first edited the file.  They are not doing anything since the Mat file is doing what I wanted to do; just replace the transparency and leaving the rest alone.

I still tried to get rid of the lines of code referencing the difuse color and specular color textures but when I did that Poser stoped accepting the file so I left it alone.