Can you let me know:
* If the user registers through the standard Joomla registration process, is the link sent?
* Do you have the "Skip Joomla Activation' setting enabled in JFBConnect?
* What is the "Registration Component" in JFBConnect set to? If not "JFBConnect", please try setting it to that and see if that works.
* What Social Profile plugins do you have enabled?
Sorry for all the questions, but they'll help narrow down what could possibly be going wrong.
Thanks,
Alex