For whatever reason, the broadcast shown when a new player joins ("Welcome to the server!") doesn't appear the way I've configured it. At the moment I have it set to show nothing, but it shows something else (http://i.imgur.com/VRgZqsG.png). Also, the permissions based blacklist doesn't seem to work. When it is set to use permissions based blacklisting it ignores it and allows people to place whatever they want.
config.yml:
http://hastebin.com/qiziqutaca.coffeescript
Group Manager config:
http://hastebin.com/jadediluje.php

Thanks in advance for any help and sorry if I'm just missing something obvious :P

Have you made sure you don't have any other plugins installed which might show a welcome message?

Yes, the message is definitely coming from Essentials

Do you have EssentialsSpawn installed? How do you know that the message is coming from Essentials?

Yes I have EssentialsSpawn installed. I know it isn't coming from something else because when I set other plugins that could possibly show a welcome message to show a welcome message, it showed theirs as well as the buggy one. The only plugin that doesn't respond to configuration for the welcome message is Essentials.

@alistoriv Have you tried disabling each plugin and restarting until the message disappears?

By that, I meant try removing each one of every plugin you have installed regardless of whether they have a welcome message config option. There's a chance that another plugin might cause this to happen without you realising. Could you post a list of plugins?

I have two other plugins that could display a welcome broadcast, one of which wasn't installed when this problem first started. The other is OnTime. I'd be surprised if OnTime was conflicting with Essentials, although I could try disabling it entirely for the moment.

Ah, I see. That wouldn't be ideal considering this server is already public, although it's not out of the question.
The plugins are as follows:
BookRules (not installed until after the problem appeared)
ColoredTablist (also not installed until after)
CraftIRC
Essentials
Hawkeye
MyWarp
OnTime
VanishNoPacket
Vault
VoxelSniper
WorldEdit
WorldGuard

Have you restarted the server since changing the Essentials config? You should also try starting the server without OnTine enabled - it could be causing the message.

Closing due to inactivity. If you need further assistance, feel free to respond to this issue and we'll reopen it.