Using BackWPUp 1.1.0, I see the line "
Undefined index: maintenance" at both start and end of the job in the log. This happens with both "Check database" and "Optimize database" job types, but not on a file or database backup. It's not an issue, but I thought I'd mention it since it looks more like an error message from PHP than a log entry line.
I have made changes to the jobs and saved them since the "maintenance mode" options became available, so I don't think it's caused by an absence of a setting in the stored configuration.