I've just tried now to manually reassign it and it did not solve the problem. I've also found a little bug that in order to assign any of the Media Keys on my keyboard I first have to disable "Use the multimedia keys as global shortcuts" as they otherwise don't get caught while assigning.
EDIT: I've made a gif showing what happens when I press the Play/Pause from my keyboard http://i.imgur.com/DsiHSc0.gifv