A user in our environment does not receive any communications from JIRA, even though messages sent through admin function of Send Email do get sent to other members in his group. The default notification scheme should also be sending him emails based on assignment of issues or those he is watching, but he does not receive these communications. His email rules do not filter out communications from JIRA.
Our email system is hosted by Microsoft Online. Using Microsoft online, you can set rules for email filtering that do not show up in the Outlook desktop application. The user had created a filter removing JIRA emails from a previous installation. The rule was removed and emails are now showing. This was a user error and JIRA is functioning correctly. Thanks for all the input!!
I had a somewhat similar problem and found that there were two usernames with the same email address and that caused subtle issues. In my case a user had been enrolled in the local "internal" directory with one username, and in a connected LDAP directory under a different username. When that user attempted to send email into JIRA the first matched email address would determine authorization, and, that username whose email address was matched first no longer had authorization (was not a member of jira-user), so the incoming email was ignored.
I know this is not your symptom but it seems like it might be worth ruling out the possibility of multiple usernames mapping to an email address because there are potential complications.
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