Nomad,
Sorry for the delayed response. I missed these follow-ups in the pre-sales area.
Are you integrating JFBConnect with another social extension right now (Community Builder or JomSocial)? I don't believe we prevent the standard New User email from being sent if you're not integrating, but I can check. Sometimes, those other components will try to hijack the new user email and send it themselves though, so this will help us narrow down where the issue is from.
Thanks!