So I made some custom clothing in Blender. Basically I started with a clean mesh (skeleton deleted and all that jazz) imported two vanilla outfits, made a few tweaks.

Then I imported a clean skeleton for the outfit and the skin bits. Once everything was exported again I used Nifty to do whatever it is nifty does with the partitions and then added textures in nifskope.

In the GECK the outfit looked okay but the boots were purple (not blue like I textured them) and everything was shiny even though I know I normal mapped it correctly.

Thinking it was just a glitch I loaded the outfit onto an npc. But now the whole outfit is using a skin texture despite the fact it shows up fine in nifskope. This happens both in the GECK preview window, and in game, but only when added to an NPC.

I'm at my wits end with what to do so any help at all would be greatly appriciated, thanks! =]