diff --git a/keymaps/base.cson b/keymaps/base.cson
index 976db68d8..938a4ee0d 100644
--- a/keymaps/base.cson
+++ b/keymaps/base.cson
@@ -23,11 +23,11 @@
   'cmdctrl-z': 'core:undo'
   'cmdctrl-Z': 'core:redo'
   'cmdctrl-y': 'core:redo'
+  'shift-delete': 'core:cut'
   'cmdctrl-x': 'core:cut'
   'cmdctrl-c': 'core:copy'
   'cmdctrl-v': 'core:paste'
   'cmdctrl-a': 'core:select-all'
-  'shift-delete': 'core:cut'
 
   'up'         : 'core:previous-item'
   'down'       : 'core:next-item'
diff --git a/keymaps/templates/Outlook.cson b/keymaps/templates/Outlook.cson
index ce6d4c409..ddce21b1e 100644
--- a/keymaps/templates/Outlook.cson
+++ b/keymaps/templates/Outlook.cson
@@ -4,13 +4,13 @@
 'body':
   # Windows email-specific menu items
   'cmdctrl-shift-v': 'application:change-category' # Outlook
-  'F3':           'application:focus-search'
+  'F3':              'application:focus-search'
   'cmdctrl-e':       'application:focus-search'
   'cmdctrl-f':       'application:forward'
   'cmdctrl-shift-v': 'application:change-category'
   'cmdctrl-d':       'application:delete-item'
-  'alt-backspace':'core:undo'
-  'alt-s':        'application:send-message'
+  'alt-backspace':   'core:undo'
+  'alt-s':           'application:send-message'
   'cmdctrl-r':       'application:reply'
   'cmdctrl-shift-r': 'application:reply-all'
   'cmdctrl-n' :      'application:new-message'
diff --git a/src/browser/application.coffee b/src/browser/application.coffee
index 831dbf83f..610c1767c 100644
--- a/src/browser/application.coffee
+++ b/src/browser/application.coffee
@@ -415,23 +415,19 @@ class Application
   sendCommand: (command, args...) ->
     unless @emit(command, args...)
       focusedWindow = @windowManager.focusedWindow()
-      focusedBrowserWindow = BrowserWindow.getFocusedWindow()
-      mainWindow = @windowManager.mainWindow()
-
-      if focusedWindow?
+      if focusedWindow
         focusedWindow.sendCommand(command, args...)
-      else if focusedBrowserWindow?
-        # Note: We sometimes display non-"AtomWindow" windows, for things like
-        # raw message contents. Ensure that these also get to run window commands
-        unless @sendCommandToFirstResponder(command)
-          switch command
-            when 'window:reload' then focusedBrowserWindow.reload()
-            when 'window:toggle-dev-tools' then focusedBrowserWindow.toggleDevTools()
-            when 'window:close' then focusedBrowserWindow.close()
-      else if mainWindow?
-        mainWindow.sendCommand(command, args...)
       else
-        @sendCommandToFirstResponder(command)
+        unless @sendCommandToFirstResponder(command)
+          focusedBrowserWindow = BrowserWindow.getFocusedWindow()
+          mainWindow = @windowManager.mainWindow()
+          if focusedBrowserWindow
+            switch command
+              when 'window:reload' then focusedBrowserWindow.reload()
+              when 'window:toggle-dev-tools' then focusedBrowserWindow.toggleDevTools()
+              when 'window:close' then focusedBrowserWindow.close()
+          else if mainWindow
+            mainWindow.sendCommand(command, args...)
 
   # Public: Executes the given command on the given window.
   #
diff --git a/src/keymap-utils.coffee b/src/keymap-utils.coffee
index a503a56fc..92e197ec3 100644
--- a/src/keymap-utils.coffee
+++ b/src/keymap-utils.coffee
@@ -1,20 +1,16 @@
 KeymapUtils =
   cmdCtrlPreprocessor: (keymap={}) ->
     re = /(cmdctrl|ctrlcmd)/i
+    if process.platform is "darwin"
+      cmdctrl = 'cmd'
+    else
+      cmdctrl = 'ctrl'
+
     for selector, keyBindings of keymap
       normalizedBindings = {}
       for keystrokes, command of keyBindings
-        if re.test keystrokes
-          if process.platform is "darwin"
-            newKeystrokes1= keystrokes.replace(re, "ctrl")
-            newKeystrokes2= keystrokes.replace(re, "cmd")
-            normalizedBindings[newKeystrokes1] = command
-            normalizedBindings[newKeystrokes2] = command
-          else
-            newKeystrokes = keystrokes.replace(re, "ctrl")
-            normalizedBindings[newKeystrokes] = command
-        else
-          normalizedBindings[keystrokes] = command
+        keystrokes = keystrokes.replace(re, cmdctrl)
+        normalizedBindings[keystrokes] = command
       keymap[selector] = normalizedBindings
 
     return keymap
diff --git a/src/menu-manager.coffee b/src/menu-manager.coffee
index 91ed99a01..dc3f7c9f8 100644
--- a/src/menu-manager.coffee
+++ b/src/menu-manager.coffee
@@ -64,6 +64,7 @@ class MenuManager
     @pendingUpdateOperation = null
     @template = []
     atom.keymaps.onDidLoadBundledKeymaps => @loadPlatformItems()
+    atom.keymaps.onDidReloadKeymap => @update()
     atom.packages.onDidActivateInitialPackages => @sortPackagesMenu()
 
   # Public: Adds the given items to the application menu.
@@ -165,7 +166,7 @@ class MenuManager
     for key, bindings of keystrokesByCommand
       for binding in bindings
         continue if binding.indexOf(' ') != -1
-
+        continue unless /(cmd|ctrl|shift|alt)/.test(binding)
         filtered[key] ?= []
         filtered[key].push(binding)
     filtered