Was having similar problems as y'all - game telling me activated things weren't activated, and CTD during the loading screen. What fixed it was installing the 1.5 patch for DEF_UI, in conjunction with going into the game's new Mods panel and "activating" all of my already activated mods. The deactivated mods, conveniently, didn't show up on the game's list, so I just had to check everything. After that it worked. Hope that helps someone.