Just to provide some clarification, JetBackup does not run the mysqlcheck command during the backup process. Your script appears to be correct, and I was able to verify this on a test environment. If you want this to run before your backup job you can go to Hooks > Create New Hook > Hook Position Pre > Hook Type Backup > Hook Script /hooks/mysqlchek.sh. Additionally, if you'd only like this script to run prior to specific backup jobs you have the option to set these here as well.