And again, but this time I might have found out why...

scripts/mysql_setup.sh

@@ -1,2 +1,3 @@
 #!/bin/bash
-mysql -h 127.0.0.1 -P 3306 --protocol=tcp -u root -e /scripts/mysql_secure_install_equivalent.sql
+service mysql start
+mysql -u root -e /scripts/mysql_secure_install_equivalent.sql