When I create users & sites in the admin it works fine and sends emails.
I'm testing and found that as a user when I try to sign up just the user account or with a site:
o) It appears to work and says that a link has been emailed to you. The user account exists in wp_signups but it isn't visible in the users list in the admin area.
o) No confirmation emails are sent
o) You can't create another user with this email until you delete the wp_signups record
o) The site doesn't seem to have been created and isn't accessible from the sites list
As I mentioned at the start all aspects of this process work from the back end so I know that it can send emails, create users & sites.
I have the "Both sites and user accounts can be registered" set in the network settings.
I have already given support access so please feel free to login and take a look.