Located in the WTF folder, your saved variables are nested. Whenever you download an interface compilation, you get some WTF files to make sure everything goes as intended. Looking at my own, I see .lua.bak files. What are they? How come compilations don't include them?
Those are just backups. When you log out the game saves the last saved variables files as backups and creates new ones. The game doesn't actually use them but you have something to roll back to if something goes wrong.