I tried changing that flag and it didn't seem to have an impact by itself. The template worked no issue with the newer app at least. The container I'm using show multiple instances of the same .dds so I tried changing all of them to transparent. The texture I injected had a completely white alpha channel, just to make sure it's not that.
That Noesis plugin is awesome. On the subject of skeleton rotation, any chance the translation can be applied somehow to the 3dsmax script. One of the mods I really want to do involves a rotated model and replaced one of the meshes from one that is not. The info on coregrafx at the time was limited as is my knowledge on the 3D structure to know which values needed changing.


