If you have investigated the html-code of the EmWiApp.html, you can see that the WebGL GUI of the Embedded Wizard works within the <CANVAS>-tag only.
Since the GUI is still downloading... you need to solve this native manually via your own js/html code.
Just a simple solution (of many):
You could just set this <CANVAS> to invisible as long as it is not ready. In addition you can add a text or image (e.g. splashscreen with a spinner-gif) that tells the user that it is loading.
After everythng is set up, you can remove the text/image and make the <CANVAS> visible again.
Code could look like this:
<META http-equiv="Content-Type" content="text/html; charset=utf-8">
<META name="Generator" content="Embedded Wizard, Tara Systems GmbH, written by Paul Banach and Manfred Schweyer">
<div id='loading' >Loading</div>
<CANVAS id="_canvas_EmWiApp" width="1350" height="480" tabindex="1" style='display: none;'>
Sorry, your browser doesn't support the canvas element.
The "display: none" makes the CANVAS invisible. Now you just need a mechanism to know when everything is downloaded. Maybe something like jQuery.ready() could help or statically via a timer (e.g. http://jsfiddle.net/MrPolywhirl/cbLsc81f/ ). Maybe your Application.init() can also tell when the GUI is fully loaded. Then just remove the loading-div and enable the CANVAS again.
Hope this helps,