by Bente Olsen.
Now I have tried to backup some courses with admin/cli/backup.php. They all went smooth.
I tried the largest course and some courses that seem to use to take a long time to backup. In addition I found some log files in temp/backup with an error: "Orphan course module (id: 400) found. This module will not be backed up." I tried to backup courses which backup file time stamp were similar to the time stamp of the log file. All went smooth, nothing obscure found with watch "ls -lR", and only empty log files were created.