Actually, this one was a bit tricky. I didn’t realize that notifications work slightly different with organizations. Sorry, I really forgot about this question and I can’t tell you exactly how to configure it as this was a while ago – but if you stumble over this, and you are trying to get notifications for issues that are in organization projects, you should read this:
whose key point is (a quote from Github support):
Users in the Owners group don’t receive notifications. You need to create a normal team and add yourself to it to get notifications for that team’s repos.