We just upgraded from JIRA 4.1.2 to 5.0.2. We also upgrade Crowd from 2.0.7 to 2.4.1. We are noticing that some of our users are no longer able to move tickets through the workflow (i.e., cannot close) that used to be able to do so. We have the Admin Helper plugin working and it identifies that the user does not have permissions to close because they are either not in the "Requirements Manager" group or the "Project Manager" role. However, when looking at the user's groups, we notice that they are actually a member of the "Requirements Manager" group.
I believe Jobin was on the right path in his statement that the groups had a sync issue. What we ended up doing was creating a new group and adding all of the users that had been in the old on that could no longer transition the workflow to the new one. Then we set that group up in the workflow at the transition points where the old group would have been and the users were then able to perform the tasks. It was strange because the jira-administrators group and the other associated role was still able to perform the tasks, but that old group didn't have the ability even though they were setup correctly. We removed the old group altogether and the workflow transition seems to be working fine now.
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