After quite some tinkering, I managed to solve the issue. It seems factorio-init downloads an invalid/not working copy of the headless server. I tried to manually download and set it up from the website and it worked like a charm on the first try.
Hope this helps anyone who encounters something ...

Heya.

I ran into an issue while trying to host a dedicated Factorio server on a VPS I own. It's a VPS running Ubuntu 14.04 with all the ports open.
I downloaded the factorio-init script and used it to set up the server, edited the config and ran the server through the init script. From looking at ...