Check the alpha channel in the main texture, not the _n one, to see what is covered with the palette.
To make it simple, the parts of the textures that should be colored with palettes should be done in grey scale, at least in grey/metallic/whatever tones that can have a color applied via overlay (That's kind of how palettes work), if you choose a dark red color on part of a texture that's masked for the palette, it'll likely become dark/black.
The alpha works with grey scale too in terms of opacity of the palette, if instead of white, you mark something with grey, you'll get the palette color applied with less opacity/strength.
Also, some pieces have two selectable colors, it's still handled the same way, only now, black in the alpha channel is the other color, if I remember correctly, it's been a while, you can check what palettes are assigned to each color in the alpha channel if you look at the .SHT file, they'll be in the 'PAL' chunks. The one marked with 'MAIN' or 'NIAM' will be the palette that gets applied to white, 'HUEB' or 'BEUH' will be black.
Hope that somehow solves your issue, if not, we'll figure it out.
Unsure if this will be helpful at all, especially with all the pictures down, but I repainted some of the composite textures years and years ago and posted updates about it: http://www.modthegalaxy.com/forums/thread-mod-wip-project-an-attempt-at-hd-textures
P.S. In that thread I mention TreExplorer, don't download that, use SIE if you aren't already.
P.P.S. Just cause all the images got killed in that thread, pics of the where I left things, still obvious wip, but you can see the palettes working there, or how they are. I used a tweaked inverted grey scale version of the main texture I believe for the alpha channel, to let some of the dirt through, have 'scratched paint' effects, etc, if I remember right.. http://imgur.com/a/i6O16