Actually set NBT and dmg settings to item

src/main/java/refinedstorage/container/ContainerGridFilter.java

@@ -8,10 +8,12 @@ import refinedstorage.inventory.ItemHandlerGridFilter;
 
 public class ContainerGridFilter extends ContainerBase {
     private ItemHandlerGridFilter filter;
+    private ItemStack stack;
 
     public ContainerGridFilter(EntityPlayer player, ItemStack stack) {
         super(player);
 
+        this.stack = stack;
         this.filter = new ItemHandlerGridFilter(stack);
 
         for (int i = 0; i < 9; ++i) {
@@ -21,6 +23,10 @@ public class ContainerGridFilter extends ContainerBase {
         addPlayerInventory(8, 70);
     }
 
+    public ItemStack getStack() {
+        return stack;
+    }
+
     @Override
     public ItemStack transferStackInSlot(EntityPlayer player, int index) {
         ItemStack stack = null;

src/main/java/refinedstorage/gui/GuiGridFilter.java

@@ -1,20 +1,31 @@
 package refinedstorage.gui;
 
+import net.minecraft.client.gui.GuiButton;
 import net.minecraftforge.fml.client.config.GuiCheckBox;
+import refinedstorage.RefinedStorage;
+import refinedstorage.api.storage.CompareUtils;
 import refinedstorage.container.ContainerGridFilter;
+import refinedstorage.item.ItemGridFilter;
+import refinedstorage.network.MessageGridFilterUpdate;
+
+import java.io.IOException;
 
 public class GuiGridFilter extends GuiBase {
+    private int compare;
+
     private GuiCheckBox compareDamage;
     private GuiCheckBox compareNBT;
 
     public GuiGridFilter(ContainerGridFilter container) {
         super(container, 176, 152);
+
+        this.compare = ItemGridFilter.getCompare(container.getStack());
     }
 
     @Override
     public void init(int x, int y) {
-        compareDamage = addCheckBox(x + 7, y + 41, t("gui.refinedstorage:grid_filter.compare_damage"), false);
-        compareNBT = addCheckBox(x + 7 + compareDamage.getButtonWidth() + 4, y + 41, t("gui.refinedstorage:grid_filter.compare_nbt"), false);
+        compareDamage = addCheckBox(x + 7, y + 41, t("gui.refinedstorage:grid_filter.compare_damage"), (compare & CompareUtils.COMPARE_DAMAGE) == CompareUtils.COMPARE_DAMAGE);
+        compareNBT = addCheckBox(x + 7 + compareDamage.getButtonWidth() + 4, y + 41, t("gui.refinedstorage:grid_filter.compare_nbt"), (compare & CompareUtils.COMPARE_NBT) == CompareUtils.COMPARE_NBT);
     }
 
     @Override
@@ -33,4 +44,17 @@ public class GuiGridFilter extends GuiBase {
         drawString(7, 7, t("gui.refinedstorage:grid_filter"));
         drawString(7, 58, t("container.inventory"));
     }
+
+    @Override
+    protected void actionPerformed(GuiButton button) throws IOException {
+        super.actionPerformed(button);
+
+        if (button == compareDamage) {
+            compare ^= CompareUtils.COMPARE_DAMAGE;
+        } else if (button == compareNBT) {
+            compare ^= CompareUtils.COMPARE_NBT;
+        }
+
+        RefinedStorage.INSTANCE.network.sendToServer(new MessageGridFilterUpdate(compare));
+    }
 }

src/main/java/refinedstorage/item/ItemGridFilter.java

@@ -2,6 +2,7 @@ package refinedstorage.item;
 
 import net.minecraft.entity.player.EntityPlayer;
 import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
 import net.minecraft.util.ActionResult;
 import net.minecraft.util.EnumActionResult;
 import net.minecraft.util.EnumHand;
@@ -14,6 +15,8 @@ import refinedstorage.inventory.ItemHandlerGridFilter;
 import java.util.List;
 
 public class ItemGridFilter extends ItemBase {
+    private static final String NBT_COMPARE = "Compare";
+
     public ItemGridFilter() {
         super("grid_filter");
 
@@ -43,4 +46,16 @@ public class ItemGridFilter extends ItemBase {
 
         ItemPattern.combineItems(tooltip, items.getFilteredItems());
     }
+
+    public static int getCompare(ItemStack stack) {
+        return (stack.hasTagCompound() && stack.getTagCompound().hasKey(NBT_COMPARE)) ? stack.getTagCompound().getInteger(NBT_COMPARE) : 0;
+    }
+
+    public static void setCompare(ItemStack stack, int compare) {
+        if (!stack.hasTagCompound()) {
+            stack.setTagCompound(new NBTTagCompound());
+        }
+
+        stack.getTagCompound().setInteger(NBT_COMPARE, compare);
+    }
 }

src/main/java/refinedstorage/network/MessageGridFilterUpdate.java

@@ -0,0 +1,35 @@
+package refinedstorage.network;
+
+import io.netty.buffer.ByteBuf;
+import net.minecraft.entity.player.EntityPlayerMP;
+import net.minecraftforge.fml.common.network.simpleimpl.IMessage;
+import refinedstorage.container.ContainerGridFilter;
+import refinedstorage.item.ItemGridFilter;
+
+public class MessageGridFilterUpdate extends MessageHandlerPlayerToServer<MessageGridFilterUpdate> implements IMessage {
+    private int compare;
+
+    public MessageGridFilterUpdate() {
+    }
+
+    public MessageGridFilterUpdate(int compare) {
+        this.compare = compare;
+    }
+
+    @Override
+    public void fromBytes(ByteBuf buf) {
+        compare = buf.readInt();
+    }
+
+    @Override
+    public void toBytes(ByteBuf buf) {
+        buf.writeInt(compare);
+    }
+
+    @Override
+    public void handle(MessageGridFilterUpdate message, EntityPlayerMP player) {
+        if (player.openContainer instanceof ContainerGridFilter) {
+            ItemGridFilter.setCompare(((ContainerGridFilter) player.openContainer).getStack(), message.compare);
+        }
+    }
+}

src/main/java/refinedstorage/proxy/CommonProxy.java

@@ -58,6 +58,7 @@ public class CommonProxy {
         RefinedStorage.INSTANCE.network.registerMessage(MessageGridUpdate.class, MessageGridUpdate.class, id++, Side.CLIENT);
         RefinedStorage.INSTANCE.network.registerMessage(MessageGridDelta.class, MessageGridDelta.class, id++, Side.CLIENT);
         RefinedStorage.INSTANCE.network.registerMessage(MessageProcessingPatternEncoderClear.class, MessageProcessingPatternEncoderClear.class, id++, Side.SERVER);
+        RefinedStorage.INSTANCE.network.registerMessage(MessageGridFilterUpdate.class, MessageGridFilterUpdate.class, id++, Side.SERVER);
 
         NetworkRegistry.INSTANCE.registerGuiHandler(RefinedStorage.INSTANCE, new GuiHandler());