After hours of trying to fix the problem, I decided to clear all my mods and completely reinstall the game. Unfortunately, that didn't fix the problem. The head/body discoloration was still present on a completely NEW game on this fresh install with ZERO mods. I reinstalled THREE times this way; I deleted all the files from My Documents, dumped the whole Skyrim install folder and the folder in Appdata, turned off steam cloud and automatic updates, and purged anything else Skyrim or related to Skyrim that I know of from my system.
The freaky thing is, this mismatch shows up in the Creation Kit, too. When I change skin tones, the face and body are always one shade off each other. Both in-game, and in the kit. Which I have also reinstalled. Twice.
This is the first problem I've hit that I have not even the first idea how to deal with. I'm tired, frustrated, and have no clue what's going on. The only factors I can possibly think to blame are either the Steam Cloud or other files somehow drifting around on my computer. I wouldn't know.
I can provide screenshots if necessary.
How is this even possible?! Please, I need some expert help here!