So, when I disable a plugin using a mod manager or the official launcher it is removed from the plugins.txt file as usual, but when I start the game (loading a save or starting a new game) the disabled plugin is still loaded! What gives? The only way for me right now to actually disable a plugin is to remove it from the Data folder, but that's not how it should work. It's been a while since I've played Skyrim but this never happened before I upgraded to the last patch (I don't know if that is the cause).

EDIT: Okay I figured it out. It's because of Mod Organiser's load mechanism which was set to 'script extender', which causes Skyrim to read the plugins.txt from a different folder.