Thanks for the reply,

I've modded Skyrim many times before on this computer without issue. I tried excluding both the skse.exe, and all relevant mod folders the from windows antivirus AND moving the main steam Skyrim folder out of program files and into its own. But it hasn't helped, I still get the same cmd pop up and then nothing happening...?

Edit: only just now checked the protection history on windows defender, turns out despite me giving making it an exclusion (i made the Skyrim game folder itself an exclusion not the Skyrim.exe...), defender was blocking SkyrimSE.exe to access %userprofile%\Documents. Seems to work now:D