Listen for focus/blur on window, not document.

spec/atom/window-spec.coffee

@@ -67,7 +67,7 @@ describe "Window", ->
 
         expect(atom.native.addMenuItem).not.toHaveBeenCalled()
 
-        $(document).focus()
+        $(window).focus()
 
         expect(atom.native.addMenuItem).toHaveBeenCalled()
         expect(addedPaths).toContain('Submenu 1 > Item 1')
@@ -76,14 +76,14 @@ describe "Window", ->
 
         spyOn(atom.native, 'resetMainMenu')
 
-        $(document).blur()
+        $(window).blur()
 
         expect(atom.native.resetMainMenu).toHaveBeenCalled()
 
       it "causes the given action to be invoked when the menu item is selected", ->
         handler = jasmine.createSpy('menuItemHandler')
         window.bindMenuItem 'Submenu > Item', handler
-        $(document).focus()
+        $(window).focus()
 
         OSX.NSApp.mainMenu.itemWithTitle('Submenu').submenu.performActionForItemAtIndex(0)
 

src/atom/window.coffee

@@ -22,13 +22,13 @@ windowAdditions =
     @registerEventHandlers()
     @bindKeys()
     @bindMenuItems()
-    $(document).focus()
+    $(window).focus()
 
   shutdown: ->
     @layout.remove()
     @editor.shutdown()
-    $(document).unbind('focus')
-    $(document).unbind('focus')
+    $(window).unbind('focus')
+    $(window).unbind('blur')
     $(window).unbind('keydown')
 
   bindKeys: ->
@@ -62,8 +62,8 @@ windowAdditions =
       for pattern, action of @keyBindings
         action() if @keyEventMatchesPattern(event, pattern)
 
-    $(document).focus => @registerMenuItems()
-    $(document).blur -> atom.native.resetMainMenu()
+    $(window).focus => @registerMenuItems()
+    $(window).blur -> atom.native.resetMainMenu()
 
   registerMenuItems: ->
     for path of @menuItemActions