IMO, the lake texture is placed all over the model and the W3D importer has a problem recognizing the fact that there are two skins. As you said the W3D viewer places the normal comanche skin and then uses the lake texture to create that "shiny" cockpit.
Maybe it's just a bug so that the importer script does not recognize two layers of texture and only applies the uppermost texture on the imported model which is, unfortunately, the lake texture.
I think there is no way to get the skin displayed properly in RenX without reapplying them to the model.
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