Steps to reproduce:
- login in a tty to verify your password work fine.
- Open "User and Groups" app, go to Advanced Settings and add some privilege to your user.
- login to a new tty and see that your password doesn't work. Try with empty password and see that it works.
- run passwd $USER to set user password again and repeat 1 to 3, in order to verify the issue.
I haven't tried, yet, any other tasks from User and Groups application to see what impact they have.