I just spent several hours setting up a relatively large MO profile, and when I go to start the game (through MO, of course), none of my mods are doing anything. The main menu replacer I picked out is absent and I get the vanilla carriage start despite having Live Another Life checked in the left pane. TES5Edit has no problems bringing up my load order, and the same goes for Wrye Bash, LOOT, and even Skyrim Launcher.exe (which is not how I normally launch the game, I did so merely to check the data files menu). My mods path is set correctly, though if it wasn't, those other programs wouldn't have access to the mods either. This is not a permission problem, as I have all of my games installed in C:\Games, away from Windows' permission jurisdiction. I am launching the game via MO's SKSE shortcut, and MO's exe file is set to run as an administrator.
I feel like I've tried everything but restarting the pc.