I used the newest release which should be compatible with 1.4.5 R0.3 and R0.2. Well, it's not compatible with 0.2 (which I use)!

[SEVERE] null
org.bukkit.command.CommandException: Unhandled exception executing command 'vanish' in plugin VanishNoPacket v3.13
at org.bukkit.command.PluginCommand.execute(PluginCommand.java:46)
at org.bukkit.command.SimpleCommandMap.dispatch(SimpleCommandMap.java:186)
at org.bukkit.craftbukkit.CraftServer.dispatchCommand(CraftServer.java:502)
at net.minecraft.server.NetServerHandler.handleCommand(NetServerHandler.java:985)
at net.minecraft.server.NetServerHandler.chat(NetServerHandler.java:903)
at net.minecraft.server.NetServerHandler.a(NetServerHandler.java:858)
at net.minecraft.server.Packet3Chat.handle(Packet3Chat.java:44)
at net.minecraft.server.NetworkManager.b(NetworkManager.java:290)
at net.minecraft.server.NetServerHandler.d(NetServerHandler.java:113)
at net.minecraft.server.ServerConnection.b(SourceFile:39)
at net.minecraft.server.DedicatedServerConnection.b(SourceFile:30)
at net.minecraft.server.MinecraftServer.r(MinecraftServer.java:595)
at net.minecraft.server.DedicatedServer.r(DedicatedServer.java:222)
at net.minecraft.server.MinecraftServer.q(MinecraftServer.java:493)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:426)
at net.minecraft.server.ThreadServerApplication.run(SourceFile:856)
Caused by: java.lang.NoSuchMethodError: net.minecraft.server.Packet60Explosion.(DDDILjava/util/ArrayList;Ljava/lang/Object;)V
at org.kitteh.vanish.filthycalls.NMS144.sendExplosionPacket(NMS144.java:16)
at org.kitteh.vanish.VanishManager.explosionEffect(VanishManager.java:291)
at org.kitteh.vanish.VanishManager.toggleVanishQuiet(VanishManager.java:250)
at org.kitteh.vanish.VanishManager.toggleVanishQuiet(VanishManager.java:208)
at org.kitteh.vanish.VanishManager.toggleVanish(VanishManager.java:179)
at org.kitteh.vanish.VanishCommand.onCommand(VanishCommand.java:46)
at org.bukkit.command.PluginCommand.execute(PluginCommand.java:44)

Same error after the update to the latest version.
I'm using 1.4.5-R0.3-snapshot

EDIT:
Same error persist on 1.4.5-R0.2 Beta release

10:30:41 [SEVERE] Unhandled exception executing command 'v' in plugin VanishNoPacket v3.13
org.bukkit.command.CommandException: Unhandled exception executing command 'v' in plugin VanishNoPacket v3.13
at org.bukkit.command.PluginCommand.execute(PluginCommand.java:46)
at com.earth2me.essentials.Essentials.onCommandEssentials(Essentials.java:314)
at com.earth2me.essentials.Essentials.onCommand(Essentials.java:299)
at org.bukkit.command.PluginCommand.execute(PluginCommand.java:44)
at org.bukkit.command.SimpleCommandMap.dispatch(SimpleCommandMap.java:186)
at org.bukkit.craftbukkit.CraftServer.dispatchCommand(CraftServer.java:502)
at net.minecraft.server.NetServerHandler.handleCommand(NetServerHandler.java:985)
at net.minecraft.server.NetServerHandler.chat(NetServerHandler.java:903)
at net.minecraft.server.NetServerHandler.a(NetServerHandler.java:858)
at net.minecraft.server.Packet3Chat.handle(Packet3Chat.java:44)
at net.minecraft.server.NetworkManager.b(NetworkManager.java:290)
at net.minecraft.server.NetServerHandler.d(NetServerHandler.java:113)
at net.minecraft.server.ServerConnection.b(SourceFile:39)
at net.minecraft.server.DedicatedServerConnection.b(SourceFile:30)
at net.minecraft.server.MinecraftServer.r(MinecraftServer.java:595)
at net.minecraft.server.DedicatedServer.r(DedicatedServer.java:222)
at net.minecraft.server.MinecraftServer.q(MinecraftServer.java:493)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:426)
at net.minecraft.server.ThreadServerApplication.run(SourceFile:856)
Caused by: java.lang.NoSuchMethodError: net.minecraft.server.Packet60Explosion.(DDDILjava/util/ArrayList;Ljava/lang/Object;)V
at org.kitteh.vanish.filthycalls.NMS144.sendExplosionPacket(NMS144.java:16)
at org.kitteh.vanish.VanishManager.explosionEffect(VanishManager.java:291)
at org.kitteh.vanish.VanishManager.toggleVanishQuiet(VanishManager.java:250)
at org.kitteh.vanish.VanishManager.toggleVanishQuiet(VanishManager.java:208)
at org.kitteh.vanish.VanishManager.toggleVanish(VanishManager.java:179)
at org.kitteh.vanish.VanishCommand.onCommand(VanishCommand.java:46)
at org.bukkit.command.PluginCommand.execute(PluginCommand.java:44)
... 18 more

Can you try out the latest dev build at ci.kitteh.org

I'll look into it.

Ignore my last post. It's working fine

the latest dev doesn't fix it

Can you please give me (pastebin.com) your full server startup log of the most recent startup where this happens, and then continue after startup to the point where this happens.