What kind of output do you get from running:
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/usr/local/nagiosxi/cron/dbmaint.php
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/usr/local/nagiosxi/cron/dbmaint.php
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CREATING: /usr/local/nagiosxi/var/dbmaint.lock
CLEANING ndoutils TABLE 'commenthistory'...
SQL: DELETE FROM nagios_commenthistory WHERE entry_time < FROM_UNIXTIME(1319400148)
CLEANING ndoutils TABLE 'processevents'...
SQL: DELETE FROM nagios_processevents WHERE event_time < FROM_UNIXTIME(1319400148)
CLEANING ndoutils TABLE 'externalcommands'...
SQL: DELETE FROM nagios_externalcommands WHERE entry_time < FROM_UNIXTIME(1350331348)
CLEANING ndoutils TABLE 'logentries'...
SQL: DELETE FROM nagios_logentries WHERE logentry_time < FROM_UNIXTIME(1343160148)
CLEANING ndoutils TABLE 'notifications'...
SQL: DELETE FROM nagios_notifications WHERE start_time < FROM_UNIXTIME(1343160148)
CLEANING ndoutils TABLE 'contactnotifications'...
SQL: DELETE FROM nagios_contactnotifications WHERE start_time < FROM_UNIXTIME(1343160148)
CLEANING ndoutils TABLE 'contactnotificationmethods'...
SQL: DELETE FROM nagios_contactnotificationmethods WHERE start_time < FROM_UNIXTIME(1343160148)
CLEANING ndoutils TABLE 'statehistory'...
SQL: DELETE FROM nagios_statehistory WHERE state_time < FROM_UNIXTIME(1287864148)
CLEANING ndoutils TABLE 'timedevents'...
SQL: DELETE FROM nagios_timedevents WHERE event_time < FROM_UNIXTIME(1350935848)
CLEANING ndoutils TABLE 'systemcommands'...
SQL: DELETE FROM nagios_systemcommands WHERE start_time < FROM_UNIXTIME(1350935848)
CLEANING ndoutils TABLE 'servicechecks'...
SQL: DELETE FROM nagios_servicechecks WHERE start_time < FROM_UNIXTIME(1350935848)
CLEANING ndoutils TABLE 'hostchecks'...
SQL: DELETE FROM nagios_hostchecks WHERE start_time < FROM_UNIXTIME(1350935848)
CLEANING ndoutils TABLE 'eventhandlers'...
SQL: DELETE FROM nagios_eventhandlers WHERE start_time < FROM_UNIXTIME(1350935848)
LASTOPT: 1350936001
INTERVAL: 60
NOW: 1350936148
OPTTIME: 1350939601
CLEANING nagiosxi TABLE 'commands'...
SQL: DELETE FROM xi_commands WHERE processing_time < 1350907348::abstime::timestamp without time zone
CLEANING nagiosxi TABLE 'events'...
SQL: DELETE FROM xi_events WHERE processing_time < 1350907348::abstime::timestamp without time zone
SQL1: SELECT xi_meta.meta_id FROM xi_meta LEFT JOIN xi_events ON xi_meta.metaobj_id=xi_events.event_id WHERE metatype_id='1' AND event_id IS NULL
SQL2: DELETE FROM xi_meta WHERE meta_id IN (SELECT xi_meta.meta_id FROM xi_meta LEFT JOIN xi_events ON xi_meta.metaobj_id=xi_events.event_id WHERE metatype_id='1' AND event_id IS NULL)
CLEANING nagiosxi TABLE 'auditlog'...
SQL: DELETE FROM xi_auditlog WHERE log_time < 1348344148::abstime::timestamp without time zone
CLEANING nagiosql TABLE 'logbook'...
SQL: DELETE FROM tbl_logbook WHERE time < FROM_UNIXTIME(1350907348)
Repair Complete: Removing Lock File