To fix the black flags:
Go to your "Documents\Paradox Interactive\Crusader Kings II" folder and delete the GFX folder. Starting the game should then generate new flags.
I'm not sure about your second issue. If you delete the GFX folder, is it still there?
Go to your "Documents\Paradox Interactive\Crusader Kings II" folder and delete the GFX folder. Starting the game should then generate new flags.
I'm not sure about your second issue. If you delete the GFX folder, is it still there?