I suppose that is caused by the emulator setting the focus on the screen when it starts, so the user can interact with it. It is designed this way.
Sorry, but I think there is no way of avoiding this right now, unless you tell the emulator not to start when the page loads.
But then you will have to provide you own way for the user to start the emulator.
Making the emulator "not start" by changing the AUTO_START property is different from simply "not powering the machine on". If you tell it not to start, it will not even display its interface on your page until you call the Javatari.start() method.
Peccin