Consolidate Multiple Textures per Object

Hello all. 

I have written a script that will consolidate all of my textures per scene, (if
it is using the same video, UV scale, translation etc. it will choose one of the
textures and apply that to all similar objects). My problem is that if I have an
object with 2 texture maps applied, the first with no alpha channel and the
second with an alpha channel to be laid over the first, after the script runs
only the second texture with an alpha channel appears on the object. When I
look, both textures are applied to the object but the display only shows one. If
I disconnect the textures and then manually reapply them, the object appears
correctly. I can't seem to figure this out. 

I searched the forums and found a similar thread that mentioned changing the
alpha to 0. I have tried this and it doesn't work. Both texture layers are set
to Translucent blend mode.