In the past there have been issues with generating the config files using FreeBSD. They have been incomplete. Please check the content if you have not done so already. As far as I remember the FreeBSD workaround has been to copy it out of the i3 example directory or so. Good luck!
If everything has worked well before that you can ignore my post. This issue was related to the configuration of the window manager during setup or when the configuration file has been re-generated. Some key code or so could not been interpreted and than the process of generating a config file stopped immediately. The result has been an incomplete non working config.