I have exactly the same problem (same versions and configuration as rad ) - however
Although I set up the registration for email confirmation, the front end reply to the user is that a mail is sent, but no registration link mail arrives.
The new user appears in the list, however as expected not confirmed, not enabled.
1) Mass mail works - (but it seems only if the new, pending user is enabled!)
2) when I (in the CB user manager) manually enable and approve the user, THEN the final confirmation email is sent and arrives.
???