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I don't know the cause, but it never hurts to run an rman "crosscheck archivelog all" and "catalog start with" to sync the standby with disk contents.
I did rman crosscheck and cataloging but it didn't help. Cataloging didn't find any unknown files to the database.
Crosscheck of course removed non-existent files from catalog.
Any thoughts on how to force this db to apply logs automatically?
You haven't given any usefuly information on your problem.
show parameter log_archive_dest
show parameter fal
show parameter dg
What errors are in your alert logs ?
What command are you using to recover ?
Check the contents of v$archived_log
# run on primary to detect failures :-
select destination, status, fail_date, valid_now
where status != 'VALID' or VALID_NOW != 'YES';
# run on standby to get exact position of rollforward :-
select thread#, to_char(snapshot_time,'dd-mon-yyyy:hh24:mi'),
to_char(newest_time,'dd-mon-yyyy:hh24:mi') from V$STANDBY_APPLY_SNAPSHOT;
Are you using dataguard broker ?