My mods were not showing up. Turns out, steam was running Fallout 4 from an old default folder even though I had created a new install destination folder ages ago. NMM was properly modding the FO4 in the new folder... But, Steam was running the copy in the old folder. - I deleted the old folder. - I made sure that when I browsed the game's local files they were in the intended folder. - Uninstalled and reinstalled mods in NMM. - Ran using NMM launcher. - All the mods showed up. This may not help your situation, but maybe it does. Good luck!
