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LDAP configuration is done based on the ldaptive library's property configuration. A paragraph of ldap configuration is created in grouper-loader.properties for each LDAP endpoint, and that paragraph is referenced by the appropriate provisioners. Comments in grouper-loader.base.properties refers to these "LDAP pools" as "LDAP connections". Make sure you are pointing to a domain name with active/standby load balancing or to the primary node. Or there could be inconsistent result of results or AD conflict CNF objects if not.
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