I just updated prosites from 3.5.1 to 126.96.36.199 and the email notifications have stopped. I reverted back to 3.5.1 and they work. Ran the debugger, deactivated wp-better-emails, set monthly pricing periods (other possible related issue), and still haven't identified it.
Everything up to date. Running mainly WPMU dev: prosites, branding, support, domain mapping, multi-db etc. WP system emails continue to work all with WP Mandrill for smtp.
I've been working this setup for months now and everything is tidy. Not sure where the conflict could be other than the plugin.
Before I begin to de-activate everything, could you please run in your test environment.