There isn't a setting. We see the issue, and will figure out an appropriate option to prevent the duplicate emails from being sent. Unfortunately, this is an issue where Community Builder gets annoying by duplicating perfectly fine functionality built into Joomla.
Anyways, to disable for now, you'll have to comment out one line of code. In /components/com_jfbconnect/controllers/loginregister.php, comment out line 306:
JUtility::sendMail($mailfrom, $fromname, $email, $subject, $message);
Hope that helps, and let us know how it goes!