In some game engines (in this case Skyrim and older BGS games using DX9 texture pipeline), a DDS texture file's alpha channel is not used for transparency but for alternate material maps, such as a specular map stored in the normal map's alpha. However, when importing such a texture, Paint.net applies it as a transparency.
Is there any way to view and alter the alpha channel completely separately from the RGB image when importing a DDS? Can it then be exported back in a proper alpha-enabled DDS format? That's pretty much the only functionality I hold on to an ancient version of Photoshop for: viewing and manipulating the alpha channels separately.
