My Fallout 4 game not detecting plugins (Even fallout4.esm)

[Xiarc]

So I reinstalled Fallout 4 and modded it up and played the game but after I left the game and reopened it the next day, it wasn't detecting any of my plugins. Not even Fallout.esm which is impossible as it the game wouldn't exist without it. Found no logical fix for this and believe me I tried everything short of completely removing the game and starting again.

I don't know if this is a NMM issue or it could be related to BethINI because I only just started using it on this playthrough.

What I did notice is if you disable 1 plugin (any at all) It only detects that plugin isn't loaded yet loads every other plugin.

 

Anyone else getting this issue or could I have royally f*#@ed something up somewhere between install and modding?