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The system is working perfectly for everything except Jira System Administrator's priviledges.
I have Jira (5.2) configured with SSO with Crowd (2.5.3) and the free plugin for IWA available on your site.
I have set up crowd directory to sync with my company's AD to provide IWA authentication for users (a requirement since we are PIV enabled here and very soon we'll loose access to our passwords)
the only problem I am having is that my user no longer has access to Jira System Administration issues even though I created a jira-system-administrator group on AD and assigned myself to it. I can validate that CROWD did the sync and shows both the group and myself as a member of that group.
My question is why I don't have access to system administrator functionality?
thanks Eddie and Harry.. you're both right. While using Jira stand alone, the groups on the local jira "directory" was being used, even though the users were coming from AD. But when we plugged in Crowd, I could no longer add users to groups other than AD and I created the groups with slight different names on AD, causing all the trouble.
I think jira-administrator and not jira-system-administrator is the role you want.