Automatic Registration is different than activation. When enabled means that when a user clicks on the Login with FB (or other social network) button, the new user is automatically created. When disabled, the user goes through a mini registration process.
Activation is controlled by different options. Please try setting the 'Skip Joomla User Activation' setting to No. JFBConnect should then respect the Joomla activation setting. If you're using a third-party extension that has activation features such as Community Builder, you may also need to go into the JFBConnect > Profiles area and set additional activation options.
-Melissa