For anyone else facing this issue, I found the cause.

The config file for factorio-init was still launching the server with hard coded peer-to-peer enabled as well as some other settings.

I changed the INVOCATION command from

INVOCATION="${BINARY} --start-server ${SAVE_NAME} --autosave-interval ...

Hi,

I have followed the Linux headless server instructions to have the latest version (factorio_headless_x64_0.12.26.tar) running on a newly set up Ubuntu Server 14.04.4 LTS.

I am having the same issues as the following supposedly resolved issue
https://forums.factorio.com/viewtopic.php?f=11&t ...

Hi,

I have followed the Linux headless server instructions to have the latest version (factorio_headless_x64_0.12.26.tar) running on a newly set up Ubuntu Server 14.04.4 LTS.

I am having the same issues as this thread, where anyone can connect to the server without issues, but when a second player ...