Media keys not working for me either. 2014 MacBook Pro. El Capitan 10.11.6.
Really I wanted the apple wired keyboard, but since no longer available I went for the forced upgrade.
Was pretty excited to open the box and hook up. When I connect my fancy new Magic Keyboard, Keyboard Setup Assistant does not recognize it, but does offer to set it up as JIS (Japanese). That however does not help.
Then, in total amazement, I discover my most desired keys, the Volume UP and DOWN do not work. Although the Volume UP key does activate "Show Desktop" from Mission Control.
None of the other function keys work. Play, pause, Mission Control, Brightness, none of them actually do anything. Although Keyboard Viewer does show them as taking input but I guess it is going nowhere.99
In Apple's defense, the box does say (in micro lettering) requires OS X 10.12.4. In my defense, come on, this is is a keyboard. IT SHOULD JUST WORK.