I am having the same problem, posting here in hopes that a solution is found. I have uninstalled the mods, NMM, and Fallout 4 and reinstalled them. I don't have any conflicting plugins and have double checked all .ini codes needed. Some of the mods activate but most are still not activating in the game, both with a currently saved game and a brand new save file. NMM plugins show all as active and non with missing .esm/.esp required files. I should also add that I am having no problems with my mods in Skyrim.