It appears that once you set a dir to non-index in cpanel that when you change it back to standard settings cpanel does not fully clean up after itself and leaves an htaccess file in the directory, in this case the words All Options was in it........... the 'code checked' part came from a hook we are working on.....
did learn however that hooks are included in every system call....
Do still have a concern over how to hide the hooks folder
any ideas????