I've done some digging and it's actually an Kitkat feature called immersive mode. You can get the buttons to show up by swiping.
I tested more apps and not all are patched to support that, that's correct.
I've just bought a Nexus 5 and this is my first vanilla Android phone, so I didn't know this is a new feature. All of my previous phones had separate buttons (HTC & Samsung).
But I hope this feature will be patcher to AppGameKit v1 also.
My AppGameKit project: http://forum.thegamecreators.com/?m=forum_view&t=206794&b=48