In order for the patches to work for you you must:
Make sure the game is patched correctly.
Start a new game. Do not load a saved game.
Uninstall all mods. (Reinstall any mods that have specifically been updated to the newest patch.)
Even old sovereigns can cause issues if things were changed, so it's also a good idea to delete and recreate sovs.
Same with custom factions.
Any of the above can cause the game to act as if it's not patched.