If you configure two LDAP repositories, but have the same user in each, with the same username but different DNs, then they have membership only of the groups in the first repository.

This is because the membership query in the second repository uses the DN from the first repository, i.e:

conn=5 op=1 SRCH base="dc=atlassian2,dc=com" scope=2 deref=3 filter="(&(objectClass=groupOfNames)(&(objectClass=groupOfNames)(member=cn=testuser1,ou=users,ou=people,ou=functest,dc=atlassian,dc=com)))"