The "cull_hardware none" and "cull_software none" lines make the texture visible from the back of the normals, case in point when someone F3s inside of a mesh, or when the normals are reversed. If the texture in question is visible from one side but not the other, it's likely a need for the Cull_Hardware Cull_Software etc lines of code.
If the parts behind the transparency are gone, I don't know what causes that.