We have gone through a couple of JIRA upgrades and found that legacy users' user-groups are not modifiable.
It allows the action but does not reflect the removal after the action is completed.
This issue still persists in our JIRA 5.1 test environment with backup data.
Marcus from Atlassian support found that the cwd_membership table had some inconsistencies regarding the groups and directory ids of such groups.
He managed to fix all these memberships by updating the parent_id with the correct group id of the membership directory with a fairly detailed query.
It is currently leveraging Active Directory.
This only happens for users that at one point have been disabled, even after re-enabling they are still left in a stale state.
Adding and removing new groups is allowed, however, removal of older groups (prior to being disabled) are not.
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