I don't know if this is your solution, but I had the weirdest issue with the GOG copy.    The game's installation files are more recent than the mods you're using, and therefore when the game opens, your skeleton is replaced by the vanilla one since that one is "newer". One of my body mods just refused to work until I downloaded a software that allowed me to edit the date of the files. The solution is explained here in this post, look for the comment that says ***SOLUTION***.