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 JIRA has a 'Group Y', but its membership is obsolete (only showing previous members, not 'bob').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.