diff --git a/app/src/processing/app/Base.java b/app/src/processing/app/Base.java
index f8bf8f5de..cb2d25d5d 100644
--- a/app/src/processing/app/Base.java
+++ b/app/src/processing/app/Base.java
@@ -1167,6 +1167,7 @@ public class Base {
 
     // The first custom menu is the "Board" selection submenu
     JMenu boardMenu = new JMenu(_("Board"));
+    boardMenu.putClientProperty("removeOnWindowDeactivation", true);
     MenuScroller.setScrollerFor(boardMenu);
     @SuppressWarnings("serial")
     Action runInstaller = new AbstractAction(_("Boards Manager...")) {
@@ -1190,13 +1191,16 @@ public class Base {
     boardMenu.add(new JSeparator());
 
     // Generate custom menus for all platforms
-    Set<String> titles = new HashSet<String>();
+    Set<String> customMenusTitles = new HashSet<String>();
     for (TargetPackage targetPackage : BaseNoGui.packages.values()) {
-      for (TargetPlatform targetPlatform : targetPackage.platforms())
-        titles.addAll(targetPlatform.getCustomMenus().values());
+      for (TargetPlatform targetPlatform : targetPackage.platforms()) {
+        customMenusTitles.addAll(targetPlatform.getCustomMenus().values());
+      }
     }
-    for (String title : titles) {
-      boardsCustomMenus.add(new JMenu(_(title)));
+    for (String customMenuTitle : customMenusTitles) {
+      JMenu customMenu = new JMenu(_(customMenuTitle));
+      customMenu.putClientProperty("removeOnWindowDeactivation", true);
+      boardsCustomMenus.add(customMenu);
     }
 
     List<JMenuItem> menuItemsToClickAfterStartup = new LinkedList<JMenuItem>();
@@ -1225,7 +1229,7 @@ public class Base {
 
         // Cycle through all boards of this platform
         for (TargetBoard board : targetPlatform.getBoards().values()) {
-          JMenuItem item = createBoardMenusAndCustomMenus(menuItemsToClickAfterStartup,
+          JMenuItem item = createBoardMenusAndCustomMenus(boardsCustomMenus, menuItemsToClickAfterStartup,
                                                           buttonGroupsMap,
                                                           board, targetPlatform, targetPackage);
           boardMenu.add(item);
@@ -1245,7 +1249,7 @@ public class Base {
   }
 
   private JRadioButtonMenuItem createBoardMenusAndCustomMenus(
-          List<JMenuItem> menuItemsToClickAfterStartup,
+          final List<JMenu> boardsCustomMenus, List<JMenuItem> menuItemsToClickAfterStartup,
           Map<String, ButtonGroup> buttonGroupsMap,
           TargetBoard board, TargetPlatform targetPlatform, TargetPackage targetPackage)
       throws Exception {
@@ -1262,7 +1266,7 @@ public class Base {
     Action action = new AbstractAction(board.getName()) {
       public void actionPerformed(ActionEvent actionevent) {
         selectBoard((TargetBoard)getValue("b"));
-        filterVisibilityOfSubsequentBoardMenus((TargetBoard)getValue("b"), 1);
+        filterVisibilityOfSubsequentBoardMenus(boardsCustomMenus, (TargetBoard)getValue("b"), 1);
 
         onBoardOrPortChange();
         rebuildImportMenu(Editor.importMenu);
@@ -1315,8 +1319,8 @@ public class Base {
     return item;
   }
 
-  private void filterVisibilityOfSubsequentBoardMenus(TargetBoard board,
-                                                             int fromIndex) {
+  private void filterVisibilityOfSubsequentBoardMenus(List<JMenu> boardsCustomMenus, TargetBoard board,
+                                                      int fromIndex) {
     for (int i = fromIndex; i < boardsCustomMenus.size(); i++) {
       JMenu menu = boardsCustomMenus.get(i);
       for (int m = 0; m < menu.getItemCount(); m++) {
@@ -1345,9 +1349,11 @@ public class Base {
   }
 
   private JMenu getBoardCustomMenu(String label) throws Exception {
-    for (JMenu menu : boardsCustomMenus)
-      if (label.equals(menu.getText()))
+    for (JMenu menu : boardsCustomMenus) {
+      if (label.equals(menu.getText())) {
         return menu;
+      }
+    }
     throw new Exception("Custom menu not found!");
   }
 
diff --git a/app/src/processing/app/Editor.java b/app/src/processing/app/Editor.java
index ba06421f3..63f253c38 100644
--- a/app/src/processing/app/Editor.java
+++ b/app/src/processing/app/Editor.java
@@ -28,7 +28,6 @@ import cc.arduino.view.*;
 import cc.arduino.view.Event;
 import cc.arduino.view.EventListener;
 import com.jcraft.jsch.JSchException;
-
 import jssc.SerialPortException;
 import processing.app.debug.*;
 import processing.app.forms.PasswordAuthorizationDialog;
@@ -184,7 +183,6 @@ public class Editor extends JFrame implements RunnerListener {
     // When bringing a window to front, let the Base know
     addWindowListener(new WindowAdapter() {
         public void windowActivated(WindowEvent e) {
-//          System.err.println("activate");  // not coming through
           base.handleActivated(Editor.this);
           // re-add the sub-menus that are shared by all windows
           fileMenu.insert(sketchbookMenu, 2);
@@ -201,12 +199,20 @@ public class Editor extends JFrame implements RunnerListener {
         // added for 1.0.5
         // http://dev.processing.org/bugs/show_bug.cgi?id=1260
         public void windowDeactivated(WindowEvent e) {
-//          System.err.println("deactivate");  // not coming through
           fileMenu.remove(sketchbookMenu);
           fileMenu.remove(examplesMenu);
           sketchMenu.remove(importMenu);
-          for (JMenu menu : base.getBoardsCustomMenus()) {
-            toolsMenu.remove(menu);
+          List<Component> toolsMenuItemsToRemove = new LinkedList<Component>();
+          for (Component menuItem : toolsMenu.getMenuComponents()) {
+            if (menuItem instanceof JComponent) {
+              Object removeOnWindowDeactivation = ((JComponent) menuItem).getClientProperty("removeOnWindowDeactivation");
+              if (removeOnWindowDeactivation != null && Boolean.valueOf(removeOnWindowDeactivation.toString())) {
+                toolsMenuItemsToRemove.add(menuItem);
+              }
+            }
+          }
+          for (Component menuItem : toolsMenuItemsToRemove) {
+            toolsMenu.remove(menuItem);
           }
           toolsMenu.remove(serialMenu);
         }