Program: 40719
Project: 40719
Buggy source:
@SubscribeEvent public void onServerTick(TickEvent.ServerTickEvent event){
  final MinecraftServer server=FMLCommonHandler.instance().getMinecraftServerInstance();
  final World world=server.getEntityWorld();
  if (Reference.pauseForPlayers && world.playerEntities.size() > 0)   return;
  if (Reference.maxChunksLoaded <= getChunksLoaded(server))   return;
  if (!Reference.toGenerate.isEmpty()) {
    chunkQueue+=Reference.numChunksPerTick;
    while (chunkQueue > 1) {
      chunkQueue--;
      chunksGenerated++;
      ChunkPosition cp=Reference.toGenerate.poll();
      if (cp != null) {
        Utilities.generateChunk(server,cp.getX(),cp.getZ(),cp.getDimensionID());
        if (chunksGenerated % Reference.updateDelay == 0) {
          float completedPercentage=1 - (float)Reference.toGenerate.size() / (float)Reference.startingSize;
          Reference.logger.info(String.format("String_Node_Str",completedPercentage));
          cp.getICommandSender().addChatMessage(new TextComponentTranslation("String_Node_Str",completedPercentage * 100));
          ConfigurationHandler.UpdateSkipChunks();
        }
        if (cp.logToChat()) {
          cp.getICommandSender().addChatMessage(new TextComponentTranslation("String_Node_Str",cp.getX(),cp.getZ(),DimensionManager.getProviderType(cp.getDimensionID()) != null ? DimensionManager.getProviderType(cp.getDimensionID()).getName() : cp.getDimensionID()));
        }
        if (Reference.toGenerate.peek() == null) {
          TextComponentTranslation chatTranslation=new TextComponentTranslation("String_Node_Str");
          server.addChatMessage(chatTranslation);
          cp.getICommandSender().addChatMessage(new TextComponentString(chatTranslation.getUnformattedComponentText()));
        }
      }
      Reference.skipChunks++;
    }
  }
}

Fixed version (ground truth):
@SubscribeEvent public void onServerTick(TickEvent.ServerTickEvent event){
  final MinecraftServer server=FMLCommonHandler.instance().getMinecraftServerInstance();
  final World world=server.getEntityWorld();
  if (Reference.pauseForPlayers && world.playerEntities.size() > 0)   return;
  if (Reference.maxChunksLoaded <= getChunksLoaded(server))   return;
  if (!Reference.toGenerate.isEmpty()) {
    chunkQueue+=Reference.numChunksPerTick;
    while (chunkQueue > 1) {
      chunkQueue--;
      chunksGenerated++;
      ChunkPosition cp=Reference.toGenerate.poll();
      if (cp != null) {
        Utilities.generateChunk(server,cp.getX(),cp.getZ(),cp.getDimensionID());
        if (chunksGenerated % Reference.updateDelay == 0) {
          double completedPercentage=1 - (double)Reference.toGenerate.size() / (double)Reference.startingSize;
          Reference.logger.info(String.format("String_Node_Str",completedPercentage));
          cp.getICommandSender().addChatMessage(new TextComponentString(String.format("String_Node_Str",completedPercentage)));
          ConfigurationHandler.UpdateSkipChunks();
        }
        if (cp.logToChat()) {
          cp.getICommandSender().addChatMessage(new TextComponentTranslation("String_Node_Str",cp.getX(),cp.getZ(),DimensionManager.getProviderType(cp.getDimensionID()) != null ? DimensionManager.getProviderType(cp.getDimensionID()).getName() : cp.getDimensionID()));
        }
        if (Reference.toGenerate.peek() == null) {
          TextComponentTranslation chatTranslation=new TextComponentTranslation("String_Node_Str");
          server.addChatMessage(chatTranslation);
          cp.getICommandSender().addChatMessage(new TextComponentString(chatTranslation.getUnformattedComponentText()));
        }
      }
      Reference.skipChunks++;
    }
  }
}