Same issue. Driving me nuts. I started with 3.0.9 and had issue. I deleted plugin and re-installed 3.1.0 and tried Tools > Buddypress > Reinstall Emails. Still no registration email in list.
I installed Buddypress 3.1.0 fresh to a new install and I see it.
I’ve even gone so far as to take the record from wp_post from that instance and installed on broken site but php is expecting something different (getting some errors on admin page for BP emails) But the record looks legit compared to other bp email records.
I think this is still a bug for anyone who started with 3.0.9. Any Ideas so that I don’t lose all my groups / comments/ etc.?