We have a user, 'bob', who was originally a member of 'Group X' only. Recently he was added to the existing 'Group Y'. Crowd shows that 'bob' is in 'Group X' and 'Group Y' (which is correct). JIRA, despite having successfully performed incremental sync with Crowd, still shows that 'bob' is only a member of 'Group X'. JIRA has a 'Group Y', but its membership is obsolete (only showing previous members, not 'bob').
I tried manually syncing the Crowd directory in JIRA without success. I see no obvious errors in the atlassian-jira.log about 'bob' or 'Group Y', nor do I see any obvious errors in the Crowd logs.
Try removing the "Allow incremental Synchronization" flag in the Crowd directory in JIRA and then Synchronizing the directory (which will perform a full sync). After that edit the directory again and re-enable the flag.
I'm not sure what causes this yet, but I just saw a very similar behavior
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