Alright.. reading up a bit more on Github's Authentication flow and they've actually changed their permission model a little bit. Right now, we request no permissions from the user, which by default gives access to:
Grants read-only access to public information (includes public user profile info, public repository info, and gists)
If the user from Github hasn't set a public email address, then Github would not return any email address when they register and JFBConnect wouldn't be able to automatically connect the user to their Joomla account.
It looks like they've added a new scope for user:email which lets us see all email addresses for the user, even if they aren't public. We'll have to do some testing with this, but my guess is that should let you get the same email address as your previous solution.
Give us a day or so and we should have an answer for you soon on the code change required.
Thanks,
Alex