Same here after upgrading from 3.0.4, ArchLinux. Updated with removing configs/mods directories and replacing them with new ones from 3.1.2.
[rz2k@Derneuca Tekkit_Server_3.0.4]$ ./launch.sh
182 recipes
27 achievements
10:15:06 [iNFO] Starting minecraft server version 1.2.5
10:15:06 [iNFO] Attempting early MinecraftForge initialization
10:15:06 [iNFO] Completed early MinecraftForge initialization
10:15:06 [iNFO] Forge Mod Loader version 2.2.91.173 for Minecraft 1.2.5 loading
10:15:07 [iNFO] Loading mods from /home/rz2k/Tekkit_Server_3.0.4/mods
10:15:07 [iNFO] Directory weaponmod contained no mods
10:15:08 [iNFO] Forge Mod Loader has loaded 38 mods
10:15:08 [iNFO] MinecraftForge v3.3.8.152 Initialized
10:15:08 [iNFO] MinecraftForge v3.3.8.152 Initialized
10:15:08 [iNFO] [WeaponMod] Properties file read succesfully!
10:15:08 [WARNING] Configuration for mod_ComputerCraft.enableAPI_http found value 0 outside acceptable range 4.9E-324,1.7976931348623157E308
10:15:08 [iNFO] Loading ComputerCraft: To change block IDs, modify config/mod_ComputerCraft.cfg
10:15:08 [iNFO] ComputerCraft: computerBlockID 207
10:15:08 [iNFO] ComputerCraft: diskDriveBlockID 208
10:15:08 [iNFO] ComputerCraft: diskItemID 4000
10:15:08 [iNFO] CONFLICT @ -49 item slot already occupied by dan200.computer.shared.ItemComputer@6220ac02 while adding net.minecraft.server.ItemBlock@4efce9a2
10:15:08 [iNFO] ComputerCraft: Searching for RedPowerLib...
10:15:08 [iNFO] ComputerCraft: RedPowerLib and methods located.
10:15:08 [iNFO] CONFLICT @ -48 item slot already occupied by dan200.computer.shared.ItemPeripheral@2513e259 while adding net.minecraft.server.ItemBlock@3c715413
10:15:08 [iNFO] Initializing alchemy values for Equivalent Exchange..
10:15:09 [iNFO] NetherOres: loaded Macerator Recipes
10:15:09 [iNFO] Loading properties
10:15:09 [iNFO] Starting Minecraft server on *:25565
10:15:09 [WARNING] **** SERVER IS RUNNING IN OFFLINE/INSECURE MODE!
10:15:09 [WARNING] The server will make no attempt to authenticate usernames. Beware.
10:15:09 [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.
10:15:09 [WARNING] To change this, set "online-mode" to "true" in the server.properties file.
10:15:11 [iNFO] Loaded codechicken.wirelessredstone.core.CommandFreq
10:15:11 [iNFO] CONFLICT @ -15 item slot already occupied by net.minecraft.server.ItemBlock@6c8484c4 while adding codechicken.enderstorage.ItemEnderChest@70289784
10:15:11 [iNFO] CONFLICT @ -204 item slot already occupied by net.minecraft.server.ItemWithAuxData@5485cd80 while adding net.minecraft.server.ItemMobSpawner@1c76b9da
10:15:11 [iNFO] [iC2] Config loaded from /home/rz2k/Tekkit_Server_3.0.4/./config/IC2.cfg
10:15:11 [sEVERE] java.lang.IllegalArgumentException: Slot 241 is already occupied by codechicken.enderstorage.BlockEnderChest@31102445 when adding ic2.common.BlockRubSapling@1abd472d
10:15:11 [sEVERE] at net.minecraft.server.Block.<init>(Block.java:181)
10:15:11 [sEVERE] at net.minecraft.server.BlockFlower.<init>(SourceFile:11)
10:15:11 [sEVERE] at net.minecraft.server.BlockFlower.<init>(SourceFile:19)
10:15:11 [sEVERE] at net.minecraft.server.BlockSapling.<init>(BlockSapling.java:18)
10:15:11 [sEVERE] at ic2.common.BlockRubSapling.<init>(BlockRubSapling.java:14)
10:15:11 [sEVERE] at net.minecraft.server.mod_IC2.load(mod_IC2.java:289)
10:15:11 [sEVERE] at cpw.mods.fml.common.modloader.ModLoaderModContainer.init(ModLoaderModContainer.java:351)
10:15:11 [sEVERE] at cpw.mods.fml.common.Loader.modInit(Loader.java:263)
10:15:11 [sEVERE] at cpw.mods.fml.common.Loader.initializeMods(Loader.java:618)
10:15:11 [sEVERE] at cpw.mods.fml.server.FMLBukkitHandler.onLoadComplete(FMLBukkitHandler.java:142)
10:15:11 [sEVERE] at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:176)
10:15:11 [sEVERE] at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:438)
10:15:11 [sEVERE] at net.minecraft.server.ThreadServerApplication.run(SourceFile:492)
10:15:11 [sEVERE] Unexpected exception
java.lang.IllegalArgumentException: Slot 241 is already occupied by codechicken.enderstorage.BlockEnderChest@31102445 when adding ic2.common.BlockRubSapling@1abd472d
at net.minecraft.server.Block.<init>(Block.java:181)
at net.minecraft.server.BlockFlower.<init>(SourceFile:11)
at net.minecraft.server.BlockFlower.<init>(SourceFile:19)
at net.minecraft.server.BlockSapling.<init>(BlockSapling.java:18)
at ic2.common.BlockRubSapling.<init>(BlockRubSapling.java:14)
at net.minecraft.server.mod_IC2.load(mod_IC2.java:289)
at cpw.mods.fml.common.modloader.ModLoaderModContainer.init(ModLoaderModContainer.java:351)
at cpw.mods.fml.common.Loader.modInit(Loader.java:263)
at cpw.mods.fml.common.Loader.initializeMods(Loader.java:618)
at cpw.mods.fml.server.FMLBukkitHandler.onLoadComplete(FMLBukkitHandler.java:142)
at net.minecraft.server.MinecraftServer.init(MinecraftServer.java:176)
at net.minecraft.server.MinecraftServer.run(MinecraftServer.java:438)
at net.minecraft.server.ThreadServerApplication.run(SourceFile:492)
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