I do not know Flash at all, but I would guess there is some kind of event that you could handle in Javascript that indicates that the Flash object has loaded. For example, in Silverlight you can provide a JavaScript "callback" that is called once the Silverlight control is loaded.
Here is some code from my blog that shows what I mean in the case of Silverlight, hope you can translate this to a Flash equiv.
1- Give the element in the web page an ID
2- Pass the ‘onLoad’ parameter on the Silverlight application assigning a JavaScript function that will focus to application in the browser.
<object id="silverlightControl" data="data:application/x-silverlight-2," type="application/x-silverlight-2" width="100%" height="100%">
<param name="source" value="ClientBin/DragSnapDemo.xap"/>
<param name="onError" value="onSilverlightError" />
<param name="onLoad" value="silverlightControlHost_Load" />
<param name="background" value="white" />
<param name="minRuntimeVersion" value="3.0.40624.0" />
<param name="autoUpgrade" value="true" />
<a href="http://go.microsoft.com/fwlink/?LinkID=149156&v=3.0.40624.0" style="text-decoration:none">
<img src="http://go.microsoft.com/fwlink/?LinkId=108181" alt="Get Microsoft Silverlight" style="border-style:none"/>
</a>
</object>
3- Finally write the JavaScript function that is called when the Silverlight application has be loaded
function silverlightControlHost_Load(sender, args)
{
var control = document.getElementById("silverlightControl");
control.focus();
}
Update: Found the following links that might be helpful
http://kb2.adobe.com/cps/155/tn_15586.html
http://www.actionscript.org/forums/archive/index.php3/t-120307.html