Have you run MySQLtuner with super user creds?
Are you sure the DB user in moodle config actually has all priv's?
Do you know the superuser creds? If so, use them in the config.php file and try the command line backup of the troubled course.
From descriptions sounds like something messed up in that one course ... difficult to guess what!
Don't have an answer for ya!
'spirit of sharing', Ken