The cause of this issue is the Lotus Domino LDAP configuration. By default unless you change the Directory Assistance Database, the groups will be displayed from the primary directory and not the secondary directory.
As there are duplicate system groups (LocalDomainServers), then the CMN task aborts with the Primary Constraint error.
To resolve this issue you need to configure Lotus Domino to provide LDAP reads from a Secondary Directory. To do this you need to ;