as far as I could see on my own databases, using mysqldump to backup a database or table will write-protects it during action.
Better ways to backup a big database are filesystem snapshot or volume manager snapshot (if you can use them)
or the program XtraBackup which does non-locking backups for InnoDB storage.
Most likely when the cron called mysqldump backup script runs, some of the new entries are lost.
My plan was to archieve the old data periodically and keep a smaller DB on the run. This would have helped the backup process as well, yet some time would still have been used.