Curious Thespian
1) create a simple mesh with two triangles, I used Blender
2) create two material slots
3) ensure both material slots are the same, e.g. MaterialA and MaterialA
4) apply a different slot to each triangle
5) export as dae, import to SL
6) rez the object, select and apply any PBR material to the object, i.e to both faces
7) release edit mode
8) shift drag the object to copy. Both objects will now have one face no longer with the PBR material applied. This also works with making any change, e.g. to "take", "take a copy", change permissions, sell, anything.
To demonstrate this and to triage what has happening I placed two planes joined as a single object at http://maps.secondlife.com/secondlife/Wensley/181/249/3759
This is available in CMT for $0
One plane has material A&B applied to the triangles, the other has materials A&A. It is A&A that is failing. Other than the difference in the material slots the mesh is otherwise identical.
This issue does
not
occur with Blinn-Phong textures.
I have tested this in the LL release viewer, Firestorm release, Firestorm Beta and on both Aditi and Agni.
My apologies if it's the wrong category!