All files are backup up and zipped, but the database (.sql) file is empty (zero bytes). This happens on some, but not all sites.
This plugin could do with a check that cehcks if the database export file really contains data, and if not, at lease declare an error.
http://wordpress.org/extend/plugins/backupwordpress/
Hi Knut,
Could you try adding the following to your wp-config.php on one of the sites with a blank database file.
define( 'HMBKP_MYSQLDUMP_PATH', false );
That will force the backup process to use the php fallback for the database dump, I'm interested to see if that is able to backup your database.
Once you've done that, re-run the backup to see if the database is still blank.