Plugins are all disabled when launching with SKSE64 Loader EXE

I am playing on the latest version of the SSE anniversary edition and I am aware of how this broke many mods, especially SKSE mods. I checked my modlist and I don't have anything that has not been updated since this regrettable update, as it's a small modlist and the only things I want to add in but am waiting on an update/patch is racemenu and fuz ro doh.
The problem lies in with the fact whenever I launch my game all my plugins go from enabled in my mod manager NMM Community edition to disabled upon launching with the SKSE loader. I noticed this by starting a new game and I went straight to the vanilla skyrim Helgen intro when I have Alternate start installed. Checked my plugins and sure enough, everything was disabled.
Can someone please help me narrow down this issue? I just want to play some quest mods (VIGILANT and The Second Great War).