I can't be sure but isn't that the default setting? If so then there has to be something that is being reset either in the backup or restore processes. Anyway, that is where I would start. Check the setting before the backup takes place, then run the backup, Download and unzip the backup and check the XML file. Make sure the setting is the same. This way you can eliminate a process if it is not the backup.
You might want to put a bug report into the Moodle Tracker though.