Program: 143304
Project: 143304
Buggy source:
@Override public void onButtonClick(ArmourPacket packet,String name){
  boolean shouldSync=false;
  try {
    if (name.equals("String_Node_Str")) {
      if (UpgradeHandler.addUpgrade(this.getContainerStack(),this.upgrade)) {
        this.upgrade=UpgradeHandler.getResult(this.containerWrapper);
        for (int i=0; i < this.containerWrapper.getSizeInventory(); ++i) {
          ItemStack itemstack1=this.containerWrapper.getStackInSlot(i);
          if (itemstack1 != null) {
            this.containerWrapper.decrStackSize(i,1);
            if (itemstack1.getItem().hasContainerItem(itemstack1)) {
              ItemStack itemstack2=itemstack1.getItem().getContainerItem(itemstack1);
              if (itemstack2 != null && itemstack2.isItemStackDamageable() && itemstack2.getItemDamage() > itemstack2.getMaxDamage()) {
                MinecraftForge.EVENT_BUS.post(new PlayerDestroyItemEvent(this.player,itemstack2));
                continue;
              }
              if (!itemstack1.getItem().doesContainerItemLeaveCraftingGrid(itemstack1) || !this.player.inventory.addItemStackToInventory(itemstack2)) {
                if (this.containerWrapper.getStackInSlot(i) == null) {
                  this.containerWrapper.setInventorySlotContents(i,itemstack2);
                }
 else {
                  this.player.dropPlayerItemWithRandomChoice(itemstack2,false);
                }
              }
            }
          }
        }
        shouldSync=true;
      }
    }
 else     if (name.equals("String_Node_Str")) {
      shouldSync=true;
      for (int i=0; i < 9; i++) {
        this.transferStackInSlot(this.player,i);
      }
    }
 else     if (name.equals("String_Node_Str")) {
      UpgradeUtil.removeUpgrade(this.getContainerStack(),UpgradeRegistry.getUpgrade(packet.getString()));
      shouldSync=true;
    }
 else     if (name.equals("String_Node_Str")) {
      if (MiscUtil.isServer(this.player.worldObj)) {
        this.player.openGui(ModularArmour.instance,GuiHandler.RECIPE_ID,this.player.worldObj,0,0,0);
      }
    }
 else     if (name.equals("String_Node_Str")) {
      NBTHelper.createDefaultStackTag(getContainerStack());
      getContainerStack().stackTagCompound.setInteger(packet.getString(),packet.getInt());
    }
  }
 catch (  UpgradeException e) {
  }
 finally {
    this.player.inventory.mainInventory[this.containerIndex]=this.getContainerStack();
  }
  if (shouldSync) {
    this.detectAndSendChanges();
    PacketHandler.sendTo(ArmourPacket.getPacket(PacketTypes.CONTAINERSYNC).addItemStack(this.getContainerStack()),player);
  }
}

Fixed version (ground truth):
@Override public void onButtonClick(ArmourPacket packet,String name){
  boolean shouldSync=false;
  try {
    if (name.equals("String_Node_Str")) {
      if (UpgradeHandler.addUpgrade(this.getContainerStack(),this.upgrade)) {
        this.upgrade=UpgradeHandler.getResult(this.containerWrapper);
        for (int i=0; i < this.containerWrapper.getSizeInventory(); ++i) {
          ItemStack itemstack1=this.containerWrapper.getStackInSlot(i);
          if (itemstack1 != null) {
            this.containerWrapper.decrStackSize(i,1);
            if (itemstack1.getItem().hasContainerItem(itemstack1)) {
              ItemStack itemstack2=itemstack1.getItem().getContainerItem(itemstack1);
              if (itemstack2 != null && itemstack2.isItemStackDamageable() && itemstack2.getItemDamage() > itemstack2.getMaxDamage()) {
                MinecraftForge.EVENT_BUS.post(new PlayerDestroyItemEvent(this.player,itemstack2));
                continue;
              }
              if (!itemstack1.getItem().doesContainerItemLeaveCraftingGrid(itemstack1) || !this.player.inventory.addItemStackToInventory(itemstack2)) {
                if (this.containerWrapper.getStackInSlot(i) == null) {
                  this.containerWrapper.setInventorySlotContents(i,itemstack2);
                }
 else {
                  this.player.dropPlayerItemWithRandomChoice(itemstack2,false);
                }
              }
            }
          }
        }
        shouldSync=true;
      }
    }
 else     if (name.equals("String_Node_Str")) {
      shouldSync=true;
      for (int i=0; i < 9; i++) {
        this.transferStackInSlot(this.player,i);
      }
    }
 else     if (name.equals("String_Node_Str")) {
      UpgradeUtil.removeUpgrade(this.getContainerStack(),UpgradeRegistry.getUpgrade(packet.getString()));
      shouldSync=true;
    }
 else     if (name.equals("String_Node_Str")) {
      if (MiscUtil.isServer(this.player.worldObj)) {
        this.player.openGui(ModularArmour.instance,GuiHandler.RECIPE_ID,this.player.worldObj,0,0,0);
      }
    }
 else     if (name.equals("String_Node_Str")) {
      NBTHelper.createDefaultStackTag(getContainerStack());
      storage.setKey(packet.getString());
      storage.set(getContainerStack(),new Percentage(packet.getInt()));
    }
  }
 catch (  UpgradeException e) {
  }
 finally {
    this.player.inventory.mainInventory[this.containerIndex]=this.getContainerStack();
  }
  if (shouldSync) {
    this.detectAndSendChanges();
    PacketHandler.sendTo(ArmourPacket.getPacket(PacketTypes.CONTAINERSYNC).addItemStack(this.getContainerStack()),player);
  }
}