You can see your hands, and what weapon and shield you hold, right? That is all you can see in vanilla.
The vanilla skeleton.nif and all the vanilla files are in the BSAs, which the game always loads, and they cannot be overriden.
Actually, I couldn't see them.... it was all messed up.
Turns out that the Deadly Reflexes mod is what had put the skeleton.nif file there, and be re-installing the mod it all worked out.