On version 2.0.1-b460
It doesn't seem to be loading the message file at all so I can't edit the messages? If I paste an old one it, it uses it, but it isn't generating a new one.

Copy it from the jar for an up-to-date one. Also, make sure the locale setting is set in the config.

Copy it from where?
That setting is enabled.

Open the EssentialsX.jar with an archiving tool like WinRAR/7zip and extract the applicable language file into your Essentials folder. This doesn't happen automatically.

Or just download it