Stop your anti-virus. Make sure it is fully stopped so it doesn't interrupt the flag installation.
Go to: C:\Users\ <YOUR USERNAME>\Documents\Paradox Interactive\Europa Universalis IV and then delete the gfx folder.
If you already had the game open, close it and restart EUIV, confirm the flags are assigned to the correct nations.
You can also try:
- Go to Documents/Paradox Interactive/Europa Universalis IV. In there, delete the entire folder called "gfx".
- After that, edit settings.txt.
- Change the settings to: