Can you clarify? I'm not exactly sure what you mean for me to do. I have barely ever used Nifskope so please explain step by step. I also looked at the fxflamesmallsub01.dds and 02.dds and they were both just blank white (possibly transparent?) textures...
http://img703.imageshack.us/i/fxflamesmallsub01.png/ is what my fxflamesmallsub01 looks like except most all of the orange is transparent that image was flattened -> you sure you opened the correct Texture?
You need to make the Textures either White so they can be colored by secondary means -> Material Property or Vert Colors -> or make them the color scales you want blue+ whatever and use the secondary Coloring to accentuate the base texture.
I suggest doing it the second way it will look better.