Access Manager deployed as a single WAR fails to configure on Directory Server 6 with a single component root suffix, for example. dc=example. However, it works with multi component root suffix, for example dc=example,dc=com. After running the configurator with configuration datastore as Sun Java System Directory server, it is always advised to go and edit the serverconfig.xml to replace the cn=directory manager with less privileged user, such as cn=dsameuser. This user should be available in the directory server with proper access permissions to the Access Manager service tree.
Workaround: Use the multi component root suffix, for example dc=example,dc=com.