2012-07-10 15:21:38 [INFO] Starting minecraft server version 1.2.5
2012-07-10 15:21:38 [INFO] Loading properties
2012-07-10 15:21:38 [INFO] Starting Minecraft server on :25565
2012-07-10 15:21:38 [WARNING] *** SERVER IS RUNNING IN OFFLINE/INSECURE MODE!
2012-07-10 15:21:38 [WARNING] The server will make no attempt to authenticate usernames. Beware.
2012-07-10 15:21:38 [WARNING] While this makes the game possible to play without internet access, it also opens up the ability for hackers to connect with any username they choose.
2012-07-10 15:21:38 [WARNING] To change this, set "online-mode" to "true" in the server.properties file.
2012-07-10 15:21:38 [INFO] This server is running CraftBukkit version git-Bukkit-1.2.5-R4.0-b2222jnks (MC: 1.2.5) (Implementing API version 1.2.5-R4.0)
2012-07-10 15:21:38 [INFO] [BorderGuard] Loading BorderGuard v4.31
2012-07-10 15:21:38 [INFO] [LyTreeHelper] Loading LyTreeHelper v3.0-BETA
2012-07-10 15:21:38 [INFO] [Vault] Loading Vault v1.2.16-b184
2012-07-10 15:21:38 [INFO] [milkAdmin] Loading milkAdmin v1.9-07.08
2012-07-10 15:21:38 [INFO] [SpawnMob] Loading SpawnMob v3.0
2012-07-10 15:21:38 [INFO] [CustomDrops] Loading CustomDrops v2.0.5
2012-07-10 15:21:38 [INFO] [Better snow] Loading Better snow v0.2test
2012-07-10 15:21:38 [INFO] [dynmap] Loading dynmap v0.40-1180
2012-07-10 15:21:38 [INFO] [dynmap-mobs] Loading dynmap-mobs v0.18
2012-07-10 15:21:38 [INFO] [MineBackup] Loading MineBackup v5.9.3
2012-07-10 15:21:38 [INFO] [Vault] Enabling Vault v1.2.16-b184
2012-07-10 15:21:38 [INFO] [Vault][Permission] SuperPermissions loaded as backup permission system.
2012-07-10 15:21:38 [INFO] [Vault] Enabled Version 1.2.16-b184
2012-07-10 15:21:38 [INFO] Preparing level "world"
2012-07-10 15:21:38 [INFO] Default game type: 0
2012-07-10 15:21:38 [INFO] Preparing start region for level 0 (Seed: 4451150481530078061)
2012-07-10 15:21:39 [INFO] Preparing start region for level 1 (Seed: -6289752164238568293)
2012-07-10 15:21:39 [INFO] Preparing spawn area: 97%
2012-07-10 15:21:39 [INFO] [BorderGuard] Enabling BorderGuard v4.31
2012-07-10 15:21:39 [INFO] BorderGuard version 4.31 is enabled!
2012-07-10 15:21:39 [INFO] [LyTreeHelper] Enabling LyTreeHelper v3.0-BETA
2012-07-10 15:21:39 [SEVERE] Error occurred while enabling LyTreeHelper v3.0-BETA (Is it up to date?)
java.lang.NullPointerException
at net.darklikally.lytreehelper.bukkit.LyTreeHelperPlugin.setupChat(LyTreeHelperPlugin.java:219)
at net.darklikally.lytreehelper.bukkit.LyTreeHelperPlugin.onEnable(LyTreeHelperPlugin.java:126)
at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:215)
at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader.java:337)
at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManager.java:381)
at org.bukkit.craftbukkit.CraftServer.loadPlugin(CraftServer.java:256)
at org.bukkit.craftbukkit.CraftServer.enablePlugins(CraftServer.java:238)
at net.minecraft.server.MinecraftServer.t(MinecraftServer.java:381)
at net.minecraft.server.MinecraftServer.a(MinecraftServer.java:368)
at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:197)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:432)
at net.minecraft.server.ThreadServerApplication.run(SourceFile:492)
2012-07-10 15:21:39 [INFO] [milkAdmin] Enabling milkAdmin v1.9-07.08
2012-07-10 15:21:39 [INFO] [milkAdmin] Permission support enabled!
2012-07-10 15:21:39 [INFO] [milkAdmin] Banlist Files Loaded
2012-07-10 15:21:39 [INFO] [milkAdmin] Banned Nicknames: (0 nicks)
2012-07-10 15:21:39 [INFO] [milkAdmin] Banned IPs: (0 IPs)
2012-07-10 15:21:39 [WARNING] [milkAdmin] Not using RTK. Required to Start/Stop/Restart/Backup.
2012-07-10 15:21:39 [INFO] [milkAdmin] v1.9-07.08 is enabled!
2012-07-10 15:21:39 [INFO] [milkAdmin] Developed by: [Sharkiller]
2012-07-10 15:21:39 [INFO] [SpawnMob] Enabling SpawnMob v3.0
2012-07-10 15:21:39 [INFO] [milkAdmin] WebServer listening on port 8125
2012-07-10 15:21:39 [INFO] Configuration files loaded.
2012-07-10 15:21:39 [INFO] [SpawnMob] Using ops.txt!
2012-07-10 15:21:39 [INFO] [SpawnMob] Version 3.0 enabled.
2012-07-10 15:21:39 [INFO] [CustomDrops] Enabling CustomDrops v2.0.5
2012-07-10 15:21:39 [INFO] CustomDrops has been enabled with version 2.0.5
2012-07-10 15:21:39 [INFO] [Better snow] Enabling Better snow v0.2test
2012-07-10 15:21:39 [INFO] [Better snow] Checking already loaded chunks for snowy areas...
2012-07-10 15:21:39 [INFO] [dynmap] Enabling dynmap v0.40-1180
2012-07-10 15:21:39 [INFO] [dynmap] Using Bukkit Permissions (superperms) for access control
2012-07-10 15:21:39 [INFO] [dynmap] Web interface permissions only available for online users
2012-07-10 15:21:40 [INFO] [dynmap] Loaded 20 shaders.
2012-07-10 15:21:40 [INFO] [dynmap] Loaded 82 perspectives.
2012-07-10 15:21:40 [INFO] [dynmap] Loaded 12 lightings.
2012-07-10 15:21:40 [INFO] [dynmap] Web server started on address 0.0.0.0:8123
2012-07-10 15:21:40 [INFO] [dynmap] version 0.40-1180 is enabled - core version 0.40-272
2012-07-10 15:21:40 [INFO] [dynmap] Loaded 3 maps of world 'world'.
2012-07-10 15:21:40 [INFO] [dynmap] World 'world_nether' disabled
2012-07-10 15:21:40 [INFO] [dynmap] Enabled
2012-07-10 15:21:40 [INFO] [dynmap-mobs] Enabling dynmap-mobs v0.18
2012-07-10 15:21:40 [INFO] [dynmap-mobs] initializing
2012-07-10 15:21:40 [INFO] [dynmap-mobs] version 0.18 is activated
2012-07-10 15:21:40 [INFO] [MineBackup] Enabling MineBackup v5.9.3
2012-07-10 15:21:40 [INFO] [MineBackup] Using Vault as provider
2012-07-10 15:21:40 [INFO] Server permissions file permissions.yml is empty, ignoring it
2012-07-10 15:21:40 [INFO] Done (2,297s)! For help, type "help" or "?"

I've fixed that issue already ;) it's the same as issue #3

You can download the latest dev build here:
https://github.com/downloads/DarkLiKally/LyTreeHelper/LyTreeHelper-3.0beta-build-2.zip