Hello Petar,
I'm sorry I didn't give you details about the best value for ' innodb_autoinc_lock_mode' to use with bacula catalog.
Having "innodb_autoinc_lock_mode=2" is the best option for performance of bulk INSERTs (you can see some INSERT...SELECT statements in the logs you sent here).
I am not a DBA, but I would recommend you to have this value set to 2 for better performance and avoid the locks/timeouts. Please be careful with this value if you use replication (quite sure you don't need/use this for bacula catalog).
The issue you are having is related to attribute insertion in catalog after job runs. Since you are reporting this when dealing with some heavy (maybe?) simultaneous full backup jobs, you will need to have your MariaDB well tuned to get this working.
I would also recommend you to have your files pruned regularly from catalog, so this file table doesn't grow too much in the case you deal with millions of files.
You told in one of your emails: "I have enabled batch insert". It is strongly recommended to build bacula with batch insert enabled and this is the default in newer versions.
Hope this helps.
Best regards,
Ana