Peter,
The change I mentioned shouldn't affect the change the developer did. I think they're both ways of masking the issue. The biggest difference is that my change is to our extension, not core Joomla. I don't think his change should cause other issues, and likely can remain intact forever, but minor changes can always have unforeseen bugs.
For the new user email, I'm still not sure how we'd be affecting that. All I can suggest is to disable the JFBConnect System, Authentication and User plugins, temporarily, and try to register normally through Joomla. If the emails aren't sent then, it definitely isn't a JFBConnect problem. I'm not sure what would be preventing them then, but I'd check the steps I mentioned above about plugins performing redirects or otherwise altering the user registration flow.
I hope that helps,
Alex