MacOS – Support for special Natural Ergonomic Keyboard 4000 hotkeys on OS X 10.11

The reason for this is that Microsoft Keyboard Helper is somehow not being added to the Login Items by the keyboard's driver installer. However, the helper is contained inside the Microsoft Keyboard Preference Pane, so it is being run when you open it, and thus restores the full functionality of the keyboard.

The simple solution is this:

1. Open System Preferences;
2. Go to Users & Groups > {your user} > Login Items;
3. Click + icon under the Login Items list;
4. When Finder window opens, press ⇧ + ⌘ + G;
5. When a form appears, paste this into it: /Library/PreferencePanes/Microsoft Keyboard.prefPane/Contents/Resources/;
6. Select the file MicrosoftKeyboardHelper, and press Add;

That's it. The keyboard should now retain its function keys' functionality after the restart.

Two months went past, and a "legitimate" solution is nowhere to be seen. Fortunately, there is a simpler and a more radical way to solve this, and all related issues — getting rid of the crappy Microsoft drivers completely. Caps Lock, and other modifier key mappings, are easily changed in the "Keyboard" preferences. Play/Pause, Volume and Mute keys are working perfectly. All of the other media keys, and the "Zoom" slider are predictably dead, but I've never used them anyway. The "Application" or "Menu key" is mapped to ⌘ with KeyRemap4MacBook.