Thanks for the reply.
I have gone through that. It's unlikely to be UAC, Skyrim is installed in D:/steam/steamapps and mod organizer is set up straight on D:/ModOrganizer2. Also I disabled UAC just to be sure and no change.
Everything is up to date, I just downloaded and installed it all today.
Well while everything was downloaded today the one thing that wasn't installed fresh was MO2, which I just used the update button on to update an installation from a few years ago. So for thoroughness's sake I completely redownloaded it and installed a new instance of it and that seems to have fixed the issue. Sorry for wasting your time, bizarre that that fixed it. Now I wonder what was causing the old installation to be slow but oh well, it's fixed.
