After upgrade Project Roles went missing when JIRA integrate with LDAP

There is some users went missing after upgrade from JIRA 5.2.11 to 6 when integrate with LDAP (Active Directory).

Steps to reproduce the problem:

1. Setup a new JIRA 5.2.11 and integrate it with LDAP (Active Directory Server).
2. There is quite a number of users created in Microsoft Active Directory. Please see
   
3. Move the Active Directory server to the top of order list via JIRA User Directories. Please see:
   
4. Configure the Project Roles in Project Demonstration. Please see
   
5. Backup the XML data and restore to JIRA 6.0.3.
6. After finish restore, go to the Project roles of Project Demonstration. The UI show there is some users went missing, please see: