I've noticed a really unusual issue while trialing Jira. Synchronisation with LDAP (users and groups) works perfectly, except that users do not appear in a group if that group is set as their Primary Group.
Active Directory has a concept of a primary group which is mainly to provide compatibility with the Unix/Linux permissions model of owner:group. This is set to Domain Users for all of our users (this is the active directory default). Because of what I can only conclude as a bug in Jira, the Domain Users group remains unpopulated after synchronisation. If I set change the primary group of my own domain account, say to Domain Admins, and then resynchronise Jira, my account appears in the Domain Users group, but it disappears from the Domain Admins group.
I've never seen this behavior with any LDAP-integrated products. I hope my description of the issue has been clear enough. If you need any further details I'm happy to provide them.