Ok, thank you both, that not only solved my problem but made sense and helped me understand Debian better.
The (virtual) server had a froxlor instance installed, which is a web-based server administration panel seems to depend on ProFTPd.
Thanks everyone!
Froxlor (http://www.froxlor.org/) has support for nginx.
Not as much functions like Cpanel, but has everything that is needed.
And does not integrate too much into the system, so you can also fix things yourself if something breaks.
If you're after a control panel that works well with Ubuntu, I'd strongly recommend Froxlor: http://www.froxlor.org/
It is open source and free, implementing it will teach you a lot.
Don't forget an iptables based firewall, Config Server Firewall is good for advanced features.