Ie9 flash object not showing when wmode is set

I'm searching and searching but do not find any solution for this.
We're having a flex web application that is working fine until now. We're using until recently the google maps flash api, unfortunately this is already deprecated and will disappear completely in september 2014. Therefor we moved the whole integration to the js v3 api, which is working fine. The whole thing is an overlay over the application, since everything is moved to js, I added the property wmode to the object in html and set it to opaque in order to be able to layer everything. It's working fine for most people, but some (including my boss) are seeing a blank screen. Seems that nothing happens (although the swf loads), and I can not figure out why. Same browser (ie 9 or 10), same flash player version (11.6.xxx). Browser cache cleared, flash player cache cleared...
Somebody having a clue? Removing the wmode-property solves the issue, but then I'm not be able to get my map on top of the application.
The swf is definetly loading since I see calls made to the server in order to login etc. It's also not a flash player issue. The swf-file is directly accessable and rendering if done so.
Thanks
Code:
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">

<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">

<head>
    <title>${title}</title>
    <meta name="google" value="notranslate" />
    <meta http-equiv="X-UA-Compatible" content="IE=10; IE=9;"/>
    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
    
    <style type="text/css" media="screen">
        html, body { height:100%; }
        body { margin:0; padding:0; overflow:hidden; text-align:center;
               background-color: ${bgcolor}; }
        object:focus { outline:none; }
        #flashContent { display:none;}
    </style>
    
    
    
    <script src="PlusOptixSync.js" language="javascript"></script>
    
     <script language="javascript">
        function getEIDxml()
          var strXML = document.MirageApplet.readCardAsXMLString() + " ";
          return strXML;
        function setOuterSize()
            var nomWidth = 1280;
            var nomHeight = 800; // 786 viewable in fullscreen
            var actWidth = nomWidth;
            var actHeight = nomHeight + 150 - 30; // fullscreen change coeff (ruimte die we winnen door f11) - taakbalk
            window.resizeTo(actWidth, actHeight);
            //window.outerWidth = actWidth;
            //window.outerHeight = actHeight;
            //script die de F1 help functionaliteit van de browser afzet. Dit is nodig omdat IE de F1 functionaliteit van de flex applicatie onderdrukt
            document.onhelp=new Function("return false");
            window.onhelp=new Function("return false");
    </script>
    <script type="text/javascript" src="swfobject.js"></script>
    <script type="text/javascript">
        // For version detection, set to min. required Flash Player version, or 0 (or 0.0.0), for no version detection.
        var swfVersionStr = "${version_major}.${version_minor}.${version_revision}";
        // To use express install, set to playerProductInstall.swf, otherwise the empty string.
        var xiSwfUrlStr = "${expressInstallSwf}";
        var flashvars = {};
        var params = {};
        params.quality = "high";
        params.bgcolor = "${bgcolor}";
        params.allowscriptaccess = "sameDomain";
        params.allowfullscreen = "true";
        params.wmode = "transparent";
        var attributes = {};
        attributes.id = "${application}";
        attributes.name = "${application}";
        attributes.align = "middle";
        swfobject.embedSWF(
            "${swf}.swf", "flashContent",
            "${width}", "${height}",
            swfVersionStr, xiSwfUrlStr,
            flashvars, params, attributes);
        // JavaScript enabled so display the flashContent div in case it is not replaced with a swf object.
        swfobject.createCSS("#flashContent", "display:block;text-align:left;");
    </script>
      
      <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/2.0.0/jquery.min.js"></script>
      <script src="http://code.highcharts.com/highcharts.js"></script>
      <script src="http://code.highcharts.com/modules/exporting.js"></script>
      <script type="text/javascript" src="../js/util/Namespace.js"></script>
      <script type="text/javascript" src="../js/util/mirage-services.js"></script>
      <script type="text/javascript" src="../js/util/mirage-binding-utils.js"></script>
      <script type="text/javascript" src="../js/util/mirage-event-dispatcher.js"></script>
      <script type="text/javascript" src="../js/util/groeicurven-highcharts-constants.js"></script>
      <script type="text/javascript" src="../js/util/groeicurven-highcharts-theme.js"></script>
      <script type="text/javascript" src="../js/util/groeicurven-highcharts-config.js"></script>
      <script type="text/javascript" src="../js/util/groeicurven-highcharts-factory.js"></script>
      <script type="text/javascript" src="../js/util/groeicurven-highcharts-zoomer.js"></script>
      <script type="text/javascript" src="../js/util/groeicurven-highcharts-formatter.js"></script>
      <script type="text/javascript" src="../js/util/groeicurven-highcharts-prototype.js"></script>
      <script type="text/javascript" src="../js/groeicurven-events.js"></script>
      <script type="text/javascript" src="../js/groeicurven-controller.js"></script>
      <script type="text/javascript" src="../js/groeicurven-flex-bridge.js"></script>
      <script language="javascript">
            initGroeicurvenFlexBridge("${application}");
      </script>
    
    <link rel="stylesheet" href="../css/google-maps.css">
    <script src="http://maps.googleapis.com/maps/api/js?sensor=false"></script>
    <script type="text/javascript" src="http://google-maps-utility-library-v3.googlecode.com/svn/trunk/styledmarker/src/StyledMarker.js"></script>
    <script type="text/javascript" src="../js/util/cvi_busy_lib.js"></script>
    <script type="text/javascript" src="../js/google-maps-events.js"></script>
    <script type="text/javascript" src="../js/google-maps-controller.js"></script>
    <script type="text/javascript" src="../js/google-maps-mediator.js"></script>
    <script language="javascript">
        function openMaps(data)
            document.getElementById('mapsContent').style.visibility ="visible";
            document.getElementById('optionsList').style.visibility ="visible";
            document.getElementById('activeCheckboxDiv').style.visibility ="visible";
            document.getElementById('mapsContent').style.zIndex = 100;
            onLoadHandler(data);
        function adresFoundHandler(marker, filtereEnabled){
            document.getElementById('mapsContent').style.visibility ="hidden";
            document.getElementById('optionsList').style.visibility ="hidden";
            document.getElementById('activeCheckboxDiv').style.visibility ="hidden";
            document.getElementById('activeCheckbox').style.visibility ="hidden";
            document.getElementById('mapsContent').style.zIndex = 0;
            clearLocations();
            ${application}.responseGoogleMaps(marker, filtereEnabled);
    </script>
    
</head>
<body scroll="no" onLoad="setOuterSize();">
    
    <div id="flashContent">
        <p>
            To view this page ensure that Adobe Flash Player version
            ${version_major}.${version_minor}.${version_revision} or greater is installed.
        </p>
        <script type="text/javascript">
            document.write("<a href='http://www.adobe.com/go/getflashplayer'><img src='get_flash_player.gif' alt='Get Adobe Flash player' /></a>" );
        </script>
    </div>
    <noscript>
        <object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" width="${width}" height="${height}" id="${application}">
            <param name="movie" value="${swf}.swf" />
            <param name="quality" value="high" />
            <param name="bgcolor" value="${bgcolor}" />
            <param name="allowScriptAccess" value="sameDomain" />
            <param name="allowFullScreen" value="true" />
            <param name="wmode" value="transparent" />
            
            <object type="application/x-shockwave-flash" data="${swf}.swf" width="${width}" height="${height}">
                <param name="quality" value="high" />
                <param name="bgcolor" value="${bgcolor}" />
                <param name="allowScriptAccess" value="sameDomain" />
                <param name="allowFullScreen" value="true" />
            
            
                <p>
                    Either scripts and active content are not permitted to run or Adobe Flash Player version
                    ${version_major}.${version_minor}.${version_revision} or greater is not installed.
                </p>
            
                <a href="http://www.adobe.com/go/getflashplayer">
                    <img src="get_flash_player.gif" alt="Get Adobe Flash Player" />
                </a>
            
            </object>
            
        </object>
    </noscript>
    <noscript>Your browser does not support JavaScript!</noscript>
    <applet
      id ="MirageApplet"
      codebase = "AppletLibs"
      archive = "kg-eid-tools-2.6.jar,beidlib-1.1.jar,jdom-1.0.jar,joda-time-1.6.jar,commons-lang-2.4.jar"
      code     = "be.kg.mirage.MirageApplet.class"
      name     = "MirageApplet"
      hspace   = "0"
      vspace   = "0"
      style="width: 0px; height: 0px;">
        <param name="Reader" value="">
        <param name="OCSP" value="0">
        <param name="CRL" value="0">
        <param name="DisableWarning" value="true">
    </applet>
    <div id ="mapsContent">
        <h3 id="typeLabel">Google Maps</h3>
        <select id="optionsList"></select>
        <input id="searchInput" type="text"></input>
        <div id="activeCheckboxDiv">
            <input id="activeCheckbox" type="checkbox"></input>
            <label for="activeCheckbox">Toon enkel actieve locaties</label>
        </div>
        <button id="searchButton" type="button" class="secondElementButton">Zoeken</button>
        <button id="annuleerButton" type="button" class="annuleerButton">Annuleer</button>
        <ul id="locations" class="thirdElement"></ul>
        <div id="canvasMap"></div>
    </div>

This means that the SWF is written so that it only works when
embedded in a web page. When you add the SWF to the stage as a
stand-alone display object using addChild() it is not being hosted
in the web page.
You have 2 options:
1. Modify the SWF code (if possible) to remove the
ExternalInterface requirement. You can write code in your AIR
application javascript to subscribe directly to events from the SWF
using addListener() and call functions directly on the SWF object
(Flash/Actionscript is not my primary development environment... so
if I have gotten the terminology wrong I apologize, but I HAVE
written a flash application that worked as I describe). My SWF
actually works embedded in HTML or not using the code "if
(ExternalInterface.available) {
ExternalInterface.addCallback("setIsPlaying", setIsPlaying ); }"
2) Somehow add a HTMLLoader in a new child window (with
transparent = false) to the stage as a new child. I have not yet
figured out exactly how to do this, so If anyone can provide
information on how to do this, I too would be appreciative.

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