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I have Active Directory setup as my primary user directory in JIRA. Works fine most of the time. I have over 400 users and anytime a new user comes in I grant them permission by adding them to the AD group AllJIRAUsers. Out of 400+ users, all but 2 sync and show up in JIRA User Management. I haven't been able to figure out why those specific 2 users will never sync and show up in JIRA.
I would need more information about that. Is the user in the right AD groups/containers? Does it fit the filter/query in the directory settings?
If you need assistance, maybe we can help with that. Just recently we went through a user migration at one of our customer and have some experience with that.