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We're running Jira 6.2 with Crowd providing authentication services across all our Atlassian software. Crowd syncs with Active Directory, and our users can all log in to Atlassian software using their Windows logon.
When a user tries to login to Jira, the first attempt fails - a message saying "You do not have permissions to log in ....." appears above the username field in the login page. When the user then tries again with the same username and password they successfully log in.
I believe (but cannot be certain) that this behavior began after the upgrade to Jira 6.2. Confluence doesn't seem to exhibit this behavior, and neither does Stash
Has any one else had the same problem?
SSO hasn't been enabled.
Our users log on to Atlassian applications using their Windows credentials - this has been working fine until just recently.
I'm beginning to get more reports from users about permissions - one user can no longer resolve issues, an admin-level user can not assign issues.
When integrating JIRA with Crowd, the SSO is not enable by default, additional modification to seraph file is needed to enable it and some customers decide to user other softwares to provide SSO.
Do you have any kind of SSO configuration in place? I'm asking this because I see you mentioned Windows logon, perhaps are you refering to Integrated Windows Authentication?
If you have SSO enabled, can you turn it off temporarily and see if it brings any improvement?