Par contre le fait de faire le lien en popup ou pas se règle directement dans le fichier flash.

<object 
          classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" 
          codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=9,0,0,0" 
          width="166" 
          height="115" 
          id="ConferencesAteliers" 
          align="middle"
        >
        <param name="allowScriptAccess" value="sameDomain" />
        <param name="allowFullScreen" value="false" />
        <param name="movie" value="images/pictos_animes/conferencesateliers.swf?lienConferenceAtelier=index.php?option=com_content*view=article*id=7*Itemid=211" />
        <param name="quality" value="high" />
 
        <param name="bgcolor" value="#ffffff" />
        <param name="wmode" value="transparent" />
        <param name="" value="lienConferenceAtelier=index.php?option=com_content*view=article*id=7*Itemid=211" />
        <embed 
          src="flash.swf" 
          quality="high" 
          bgcolor="#ffffff" 
          width="166" 
          height="115" 
          name="ConferencesAteliers" 
          align="middle" 
          allowScriptAccess="sameDomain" 
          allowFullScreen="false" 
          type="application/x-shockwave-flash" 
          pluginspage="http://www.macromedia.com/go/getflashplayer"
          wmode="transparent"   
          flashvars="lienConferenceAtelier=index.php?option=com_content*view=article*id=7*Itemid=211"
        />
        </object>