I doubt the malware was inserted from a video file, there are certainly enough other methods to alter php files remotely.
I think you should check to ensure your Cliphouse software is up to date, and the latest version.
and find out if there are any known vulnerabilities in their code that would allow your site to be compromised.
Check the install directions for Cliphouse that outline the configuration of your server, and ensure you have all the setting done properly in your PHP, Apache, and MySQL configs.
If you have any other PHP code on your website, ensure that it too is up to date and secure..