Course not backed up with CLI script

As reported by Anna Sadia in MDLQA-14676:

Steps to reproduce:

1. Log in as an administrator.
2. Create a test course,'course1'.
3. Go to Site administration > Courses > Backups > Automated backup setup.
4. Ensure under Automated backup setup, Active (backup_auto_active) is set to Enabled.
5. Ensure under Automated backup setup, Skip courses not modified since previous backup (backup_auto_skip_modif_prev) is checked (enabled).
6. In your site's wwwroot, run: php admin/cli/automated_backups.php

Expected result: The backup runs to completion, and includes the following in the output: "Backing up coursexx...".

Actual result: "Backing up coursexx" is not reflected in the output.