MysticallyDeafeningNinja

I managed to fix it! :D I thought I had been running NMM as an admin, but it turns out I hadn't been, so I did that again, as well as actually updating the software, and one of those two things fixed the problem!

NMM will download files just fine, and it shows they're installed and enabled, but when I go into the data folder only some of the files have actually been installed, primarily just the .esp files. When I go to manually install one of the same mods, it'll say out of maybe 30 files in the mod, only one is already in the folder. In game the most obvious example of this I've been able to find is with custom weapons, It shows up in my inventory just fine, but when I take it out to shoot something the textures are missing (it's not like they're showing up as purple either, which is an issue I've encountered before, there's just no texture there, it just shows as holding air). NMM is also disabling certain mods every time I reopen NMM or boot up my game, and I have not yet been able to find a pattern to which mods get disabled. This problem first occurred after I completely uninstalled Fallout 4, deleted all leftover files associated with the game, and reinstalled (on a different drive, as since I originally installed the game I've gotten an extra drive dedicated for games to be installed on). After I first encountered this problem, I tried to manually install all of the mods, but continued to encounter the issue with some mods randomly getting disabled, so I uninstalled and deleted everything again, but this time while I was reinstalling my mods I deleted them all from NMM and rebuilt my list by downloading them all again, but this did not fix it, and looking in my data folder I once again am missing all texture/sound/interface/etc files, with only the .esp/.esl files having been installed.