package com.github.lunatrius.core;

import com.github.lunatrius.core.handler.ConfigurationHandler;
import com.github.lunatrius.core.lib.Reference;
import com.github.lunatrius.core.proxy.CommonProxy;
import com.github.lunatrius.core.version.VersionChecker;
import cpw.mods.fml.common.Mod;
import cpw.mods.fml.common.Mod.EventHandler;
import cpw.mods.fml.common.SidedProxy;
import cpw.mods.fml.common.event.FMLInitializationEvent;
import cpw.mods.fml.common.event.FMLPostInitializationEvent;
import cpw.mods.fml.common.event.FMLPreInitializationEvent;

@Mod(modid = Reference.MODID, name = Reference.NAME, guiFactory = Reference.GUI_FACTORY)
public class LunatriusCore {
	@SidedProxy(serverSide = Reference.PROXY_SERVER, clientSide = Reference.PROXY_CLIENT)
	public static CommonProxy proxy;

	@EventHandler
	public void preInit(FMLPreInitializationEvent event) {
		VersionChecker.registerMod(event.getModMetadata());

		Reference.logger = event.getModLog();
		ConfigurationHandler.init(event.getSuggestedConfigurationFile());
	}

	@EventHandler
	public void init(FMLInitializationEvent event) {
		if (ConfigurationHandler.checkForUpdates) {
			VersionChecker.startVersionCheck();
		}

		proxy.registerTickers();
	}

	@EventHandler
	public void postInit(FMLPostInitializationEvent event) {
	}
}

package com.github.lunatrius.core;

import com.github.lunatrius.core.handler.ConfigurationHandler;
import com.github.lunatrius.core.lib.Reference;
import com.github.lunatrius.core.proxy.CommonProxy;
import com.github.lunatrius.core.version.VersionChecker;
import cpw.mods.fml.common.Mod;
import cpw.mods.fml.common.Mod.EventHandler;
import cpw.mods.fml.common.SidedProxy;
import cpw.mods.fml.common.event.FMLInitializationEvent;
import cpw.mods.fml.common.event.FMLPostInitializationEvent;
import cpw.mods.fml.common.event.FMLPreInitializationEvent;

@Mod(modid = Reference.MODID, name = Reference.NAME, guiFactory = Reference.GUI_FACTORY)
public class LunatriusCore {
	@SidedProxy(serverSide = Reference.PROXY_SERVER, clientSide = Reference.PROXY_CLIENT)
	public static CommonProxy proxy;

	@EventHandler
	public void preInit(FMLPreInitializationEvent event) {
		Reference.logger = event.getModLog();
		ConfigurationHandler.init(event.getSuggestedConfigurationFile());

		VersionChecker.registerMod(event.getModMetadata(), Reference.FORGE);
	}

	@EventHandler
	public void init(FMLInitializationEvent event) {
		if (ConfigurationHandler.checkForUpdates) {
			VersionChecker.startVersionCheck();
		}

		proxy.registerTickers();
	}

	@EventHandler
	public void postInit(FMLPostInitializationEvent event) {
	}
}

Move the version checker registration to the end of preInit, make sure the logger is initialized first.