@everaejo
First a few questions:
What version number of COPS did you install?
In the file config_local.php that you copied from config_local.php.example or config_default.php did you change anything other than the line
Code:
$config['calibre_directory'] = './calibre/';
where ./caliber/ point to your calibre directory on your QNAP?
Are the files readable for all users (-rw-r--r--)? (change with chmod)
Did you change anything in .htaccess?
Can you ssh (using putty) into your QNAP?