I've also created a custom stream for emailing people and places that I choose to follow but don't necessarily want posted to my "inbox".
note i had to do this again after receipt of emails stopped on 7 July 2015
I reported this to Jive Support recently. Do you see any connection to downtime/restarts of the community?
They are asking whether you can provide a screenshot of your connection stream displaying some of the notifications that you didn't receive individual emails for. Then they can investigate those notifications.
If it's too long ago now, I can tell them to drop it -- but please let me know. Thanks!