Hello,
We are trying to help you, and as it's working with PHP CLI, we are sure the problem must come from a PHP or Apache configuration or some program such as SELinux that is blocking PHP to call the conversion plugin. Did you enable the debug option and check your server logs?
Please send to contact[at]phpdocx.com the information to connect to your server through SSH, the path where phpdocx is installed and an URL to test it using a web browser and we'll check it.
Regards.