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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.

I just reinstalled SkyrimSE and Mod Organizer 2 after a few years of not playing and a completely blank, no mods at all (other than SKSE), SkyrimSE install is hanging for about two minutes on a black screen after the Bethesda Logo. But only when it's launched from Mod Organizer 2. When launched from Steam or directly from the executable it goes straight through to the main menu instantly after the Bethesda Logo, no delay at all. Happens regardless of if I'm running with or without the script extender. The only thing I could think of was to try running MO2 as admin but that didn't change anything. Is this expected behaviour from Mod Organizer 2? I doubt it, so anyone got any ideas how I might go about debugging this before I start downloading mods?