Everytime a staff member joins vanished, a blank line appears.

How would i fix this? or is it just a bug that needs to be fixed?

I'm using GroupManager as the permissions plugin.

I need:
The output of /version
The output of /version VanishNoPacket
The output of /plugins

While I'm still unable to look into things further let's try something:

Create a test server with just these plugins (and your configs for them): GroupManager, VanishNoPacket

See if it still does it

So it didn't do it with just those two. Once i added essentials.jar it did it. It occurs between the " has joined vanished and silently" and the "Welcome, to !" from the essentials part.

Looks like Essentials is adding that message. Make sure you're on the latest version :)

Output of /version : This server is running CraftBukkit version git-Bukkit-1.7.2-R0.1-2-gf24d967-b2971jnks (MC: 1.7.2) (Implementing API version 1.7.2-R0.2-SNAPSHOT)

Output of /version VanishNoPacket:
Author: mbaxter
Website: http://kitteh.org
Vanish for the distinguished admin
VanishNoPacket version 3.18.7

Output of /plugins: Plugins (26): WorldBorder, GroupManager, WorldEdit, TokenStore, CoreProtect, chatannouncer, Buycraft, BanManager, Lockette, Vault, PlayerHeads, BlockNotif, MobArena, Entity Police, WorldGuard, Essentials, EssentialsProtect, EssentialsSpawn, WelcomeBookRecoded, VanishNoPacket, EssentialsChat, WGCustomFlags, EssentialsAntiBuild, WGKeepInventoryFlags, WGMobDamageFlags, WGSpawnPointFlag