There are some conflicting item ID's in the config file for which I noticed the following in the Java logs:

2012-12-09 16:33:40 [INFO] [STDOUT] CONFLICT @ 31742 item slot already occupied by buildcraft.transport.ItemPipe@18e3219 while adding buildcraft.transport.ItemPipe@1e7b081b
2012-12-09 16:33:40 [INFO] [STDOUT] CONFLICT @ 31743 item slot already occupied by buildcraft.transport.ItemPipe@4053debb while adding buildcraft.transport.ItemPipe@4243e7fb

All the conflicts are in the AdditionalPipes' own config file, not between other mods.
Is this expected / intended behavior? Should the item ID's collide?

Altering the ID's so that they are unique will generate a crash from AdditionalPipes as follows:

----------------- Console Log ------------------
Instance folder is:
C:\Users\AppData\Roaming\Minecraft\MultiMC\instances\1.4.5\minecraft\

Instance started with command:
"C:\Program Files\Java\jre7\bin\java.exe" -Xms512m -Xmx2048m -jar MultiMCLauncher.jar "" "" "MultiMC: 1.4.5" "854x480"

File encoding: Cp1252
Loading jars...
Loading URL: file:/C:/Users//AppData/Roaming/Minecraft/MultiMC/instances/1.4.5/minecraft/bin/minecraft.jar
Loading URL: file:/C:/Users//AppData/Roaming/Minecraft/MultiMC/instances/1.4.5/minecraft/bin/lwjgl.jar
Loading URL: file:/C:/Users//AppData/Roaming/Minecraft/MultiMC/instances/1.4.5/minecraft/bin/lwjgl_util.jar
Loading URL: file:/C:/Users//AppData/Roaming/Minecraft/MultiMC/instances/1.4.5/minecraft/bin/jinput.jar
Loading natives...
Fixed Minecraft Path: Field was private static java.io.File net.minecraft.client.Minecraft.an
Launching with applet wrapper...
2012-12-09 16:32:42 [INFO] [ForgeModLoader] Forge Mod Loader version 4.5.2.459 for Minecraft 1.4.5 loading
2012-12-09 16:32:42 [INFO] [STDOUT] Adding Accesstransformer map: codechickencore_at.cfg
2012-12-09 16:32:42 [INFO] [STDOUT] Adding Accesstransformer map: nei_at.cfg
2012-12-09 16:32:42 [INFO] [STDOUT] Inserted super call into avs.c
2012-12-09 16:32:42 [INFO] [STDOUT] auy was overriden from NotEnoughItems 1.4.2.10.jar
2012-12-09 16:32:43 [INFO] [STDOUT] Generated BlockMobSpawner helper method.
2012-12-09 16:32:43 [INFO] [STDOUT] 27 achievements
2012-12-09 16:32:44 [INFO] [STDOUT] 208 recipes
2012-12-09 16:32:44 [INFO] [STDOUT] Setting user: ,
2012-12-09 16:32:44 [INFO] [STDOUT] LWJGL Version: 2.4.2
2012-12-09 16:32:45 [INFO] [ForgeModLoader] Attempting early MinecraftForge initialization
2012-12-09 16:32:45 [INFO] [STDOUT] MinecraftForge v6.4.1.410 Initialized
2012-12-09 16:32:45 [INFO] [ForgeModLoader] MinecraftForge v6.4.1.410 Initialized
2012-12-09 16:32:45 [INFO] [STDOUT] Replaced 84 ore recipies
2012-12-09 16:32:45 [INFO] [ForgeModLoader] Completed early MinecraftForge initialization
2012-12-09 16:32:45 [INFO] [ForgeModLoader] Searching C:\Users\AppData\Roaming\Minecraft\MultiMC\instances\1.4.5\minecraft\mods for mods
2012-12-09 16:32:46 [INFO] [ForgeModLoader] Forge Mod Loader has identified 49 mods to load
2012-12-09 16:32:48 [INFO] [ForgeModLoader] Configured a dormant chunk cache size of 0
2012-12-09 16:32:50 [INFO] [Buildcraft] Starting BuildCraft 3.2.2 (:0)
2012-12-09 16:32:50 [INFO] [Buildcraft] Copyright (c) SpaceToad, 2011
2012-12-09 16:32:50 [INFO] [Buildcraft] http://www.mod-buildcraft.com
2012-12-09 16:32:50 [INFO] [IC2] Config loaded from C:\Users\AppData\Roaming\Minecraft\MultiMC\instances\1.4.5\minecraft\config\IC2.cfg
2012-12-09 16:32:51 [INFO] [ExtrabiomesXL] Intializing.
2012-12-09 16:32:51 [INFO] [ExtrabiomesXL] Module SUMMA is enabled.
2012-12-09 16:32:51 [INFO] [ExtrabiomesXL] Module CAUTIA is enabled.
2012-12-09 16:32:51 [INFO] [ExtrabiomesXL] Module FABRICA is enabled.
2012-12-09 16:32:51 [INFO] [ExtrabiomesXL] Module AMICA is enabled.
2012-12-09 16:32:52 [WARNING] [ForgeModLoader] Forestry: Using outdated version [1.6.2.3 (build:33)] for Minecraft 1.4.5. Consider updating.
2012-12-09 16:32:53 [INFO] [ForgeModLoader] [Mystcraft] Adding Entity Renderers
2012-12-09 16:32:53 [INFO] [ObsidiPlates] Config loaded from: C:\Users\AppData\Roaming\Minecraft\MultiMC\instances\1.4.5\minecraft\config\ObsidiPlates.cfg
2012-12-09 16:32:53 [INFO] [STDOUT] [Portal Gun 1.4.4v0.1] Loading properties.
2012-12-09 16:32:53 [INFO] [STDOUT] [Portal Gun 1.4.4v0.1] Properties loaded.
2012-12-09 16:32:54 [INFO] [ThermalExpansion] An updated version of Thermal Expansion is available: 2.1.1.0.
2012-12-09 16:32:54 [SEVERE] [ForgeModLoader] Fatal errors were detected during the transition from PREINITIALIZATION to INITIALIZATION. Loading cannot continue
2012-12-09 16:32:54 [SEVERE] [ForgeModLoader]
mcp Minecraft Coder Pack Unloaded->Constructed->Pre-initialized
FML Forge Mod Loader Unloaded->Constructed->Pre-initialized
Forge Minecraft Forge Unloaded->Constructed->Pre-initialized
mod_CodeChickenCore CodeChicken Core Unloaded->Constructed->Pre-initialized
mod_NotEnoughItems Not Enough Items Unloaded->Constructed->Pre-initialized
BuildCraft|Core BuildCraft Unloaded->Constructed->Pre-initialized
BuildCraft|Factory BC Factory Unloaded->Constructed->Pre-initialized
BuildCraft|Transport BC Transport Unloaded->Constructed->Pre-initialized
BuildCraft|Silicon BC Silicon Unloaded->Constructed->Pre-initialized
APUnofficial Additional Pipes Unofficial Unloaded->Constructed->Errored
IC2 IndustrialCraft 2 Unloaded->Constructed->Pre-initialized
AdvancedMachines IC2 Advanced Machines Addon Unloaded->Constructed->Pre-initialized
AdvancedSolarPanel Advanced Solar Panels Unloaded->Constructed->Pre-initialized
BuildCraft|Builders BC Builders Unloaded->Constructed->Pre-initialized
BuildCraft|Energy BC Energy Unloaded->Constructed->Pre-initialized
ComputerCraft ComputerCraft Unloaded->Constructed->Pre-initialized
CCTurtle ComputerCraft Turtles Unloaded->Constructed->Pre-initialized
EnderStorage [EnderStorage](EnderStorage 1.2.1.6.jar) Unloaded->Constructed->Pre-initialized
ExtraBees Extra Bees Unloaded->Constructed->Pre-initialized
BinnieCore Binnie Core Unloaded->Constructed->Pre-initialized
ExtrabiomesXL ExtrabiomesXL Unloaded->Constructed->Pre-initialized
Forestry Forestry for Minecraft Unloaded->Constructed->Pre-initialized
ForgeIRC ForgeIRC Unloaded->Constructed->Pre-initialized
GraviSuite Gravitation Suite Unloaded->Constructed->Pre-initialized
GregTech_Addon GregTech-Addon Unloaded->Constructed->Pre-initialized
IC2NuclearControl Nuclear Control Unloaded->Constructed->Pre-initialized
mod_InvTweaks Inventory Tweaks Unloaded->Constructed->Pre-initialized
IronChest Iron Chest Unloaded->Constructed->Pre-initialized
LogisticsPipes|Main Logistics Pipes Unloaded->Constructed->Pre-initialized
MiscPeripherals MiscPeripherals Unloaded->Constructed->Pre-initialized
ModularForceFieldSystem Modular ForceField System V2 Unloaded->Constructed->Pre-initialized
Mystcraft Mystcraft Unloaded->Constructed->Pre-initialized
NEIPlugins NEI Plugins Unloaded->Constructed->Pre-initialized
ObsidiPlates Obsidian Pressure Plates Unloaded->Constructed->Pre-initialized
PortalGun Portal Gun Unloaded->Constructed->Pre-initialized
PowerConverters Power Converters Unloaded->Constructed->Pre-initialized
Railcraft Railcraft Unloaded->Constructed->Pre-initialized
mod_ReiMinimap mod_ReiMinimap Unloaded->Constructed->Pre-initialized
SoulShards Soul Shards Unloaded->Constructed->Pre-initialized
StevesCarts Steve's Carts Unloaded->Constructed->Pre-initialized
Thaumcraft Thaumcraft Unloaded->Constructed->Pre-initialized
ThermalExpansion Thermal Expansion Unloaded->Constructed->Pre-initialized
ThermalExpansion|Factory Factory Unloaded->Constructed->Pre-initialized
ThermalExpansion|Energy Energy Unloaded->Constructed->Pre-initialized
ThermalExpansion|NEI NEI Unloaded->Constructed->Pre-initialized
mod_Timber [Timber!](Timber! %281.4.4%29.zip) Unloaded->Constructed->Pre-initialized
TwilightForest The Twilight Forest Unloaded->Constructed->Pre-initialized
WR-CBE|Core [WR-CBE Core](WR-CBE Core 1.3.1.1.jar) Unloaded->Constructed->Pre-initialized
WR-CBE|Addons [WR-CBE Addons](WR-CBE Addons 1.3.1.2.jar) Unloaded->Constructed->Pre-initialized
2012-12-09 16:32:54 [SEVERE] [ForgeModLoader] The following problems were captured during this phase
2012-12-09 16:32:54 [SEVERE] [ForgeModLoader] Caught exception from APUnofficial
java.lang.NullPointerException
at buildcraft.additionalpipes.AdditionalPipes.loadConfigs(AdditionalPipes.java:306)
at buildcraft.additionalpipes.AdditionalPipes.preInit(AdditionalPipes.java:177)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at cpw.mods.fml.common.FMLModContainer.handleModStateEvent(FMLModContainer.java:440)
at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.google.common.eventbus.EventHandler.handleEvent(EventHandler.java:69)
at com.google.common.eventbus.SynchronizedEventHandler.handleEvent(SynchronizedEventHandler.java:45)
at com.google.common.eventbus.EventBus.dispatch(EventBus.java:317)
at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:300)
at com.google.common.eventbus.EventBus.post(EventBus.java:268)
at cpw.mods.fml.common.LoadController.propogateStateMessage(LoadController.java:140)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.google.common.eventbus.EventHandler.handleEvent(EventHandler.java:69)
at com.google.common.eventbus.SynchronizedEventHandler.handleEvent(SynchronizedEventHandler.java:45)
at com.google.common.eventbus.EventBus.dispatch(EventBus.java:317)
at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:300)
at com.google.common.eventbus.EventBus.post(EventBus.java:268)
at cpw.mods.fml.common.LoadController.distributeStateMessage(LoadController.java:83)
at cpw.mods.fml.common.Loader.loadMods(Loader.java:480)
at cpw.mods.fml.client.FMLClientHandler.beginMinecraftLoading(FMLClientHandler.java:151)
at net.minecraft.client.Minecraft.a(Minecraft.java:424)
at net.minecraft.client.Minecraft.run(Minecraft.java:756)
at java.lang.Thread.run(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] java.lang.NullPointerException
2012-12-09 16:32:54 [INFO] [STDERR] at buildcraft.additionalpipes.AdditionalPipes.loadConfigs(AdditionalPipes.java:306)
2012-12-09 16:32:54 [INFO] [STDERR] at buildcraft.additionalpipes.AdditionalPipes.preInit(AdditionalPipes.java:177)
2012-12-09 16:32:54 [INFO] [STDERR] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-12-09 16:32:54 [INFO] [STDERR] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] at java.lang.reflect.Method.invoke(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] at cpw.mods.fml.common.FMLModContainer.handleModStateEvent(FMLModContainer.java:440)
2012-12-09 16:32:54 [INFO] [STDERR] at sun.reflect.GeneratedMethodAccessor3.invoke(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] at java.lang.reflect.Method.invoke(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.EventHandler.handleEvent(EventHandler.java:69)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.SynchronizedEventHandler.handleEvent(SynchronizedEventHandler.java:45)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.EventBus.dispatch(EventBus.java:317)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:300)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.EventBus.post(EventBus.java:268)
2012-12-09 16:32:54 [INFO] [STDERR] at cpw.mods.fml.common.LoadController.propogateStateMessage(LoadController.java:140)
2012-12-09 16:32:54 [INFO] [STDERR] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
2012-12-09 16:32:54 [INFO] [STDERR] at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] at java.lang.reflect.Method.invoke(Unknown Source)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.EventHandler.handleEvent(EventHandler.java:69)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.SynchronizedEventHandler.handleEvent(SynchronizedEventHandler.java:45)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.EventBus.dispatch(EventBus.java:317)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.EventBus.dispatchQueuedEvents(EventBus.java:300)
2012-12-09 16:32:54 [INFO] [STDERR] at com.google.common.eventbus.EventBus.post(EventBus.java:268)
2012-12-09 16:32:54 [INFO] [STDERR] at cpw.mods.fml.common.LoadController.distributeStateMessage(LoadController.java:83)
2012-12-09 16:32:54 [INFO] [STDERR] at cpw.mods.fml.common.Loader.loadMods(Loader.java:480)
2012-12-09 16:32:54 [INFO] [STDERR] at cpw.mods.fml.client.FMLClientHandler.beginMinecraftLoading(FMLClientHandler.java:151)
2012-12-09 16:32:54 [INFO] [STDERR] at net.minecraft.client.Minecraft.a(Minecraft.java:424)
2012-12-09 16:32:54 [INFO] [STDERR] at net.minecraft.client.Minecraft.run(Minecraft.java:756)
2012-12-09 16:32:54 [INFO] [STDERR] at java.lang.Thread.run(Unknown Source)