Im having the same exact issue with xEdit but the CK, BodySlide and SkyrimTools - Resaver are working correctly. I also found that NifSkope isnt working through MO either when I look to load a nif from SSE data folder there is nothing there if I do it with BodySlide I see the mesh and other folders there. Also when I run xEdit it puts its backup folder directly into the data folder instead of the overwrite folder like normal. All the usvfs logs are empty as well.