I've got the same problem right now. It appears NMM has problems with symlinked folders. I use SteamMover to move my active games to an SSD. Under steamapps, the Fallout 4 folder is linked to a different drive. When it's set this way NMM can manage plugins but anything that requires managing loose files fail. It will create the folder structure but none of the files get copied so the mods aren't actually loaded when the game is started. Once I use SteamMover to move the Fallout 4 directory back to my HDD. NMM works as expected.
