Normally, the workaround to that is by adding a param "wmode" and setting it to either "opaque" or "transparent" but I have found out that while I have rewritten the code so that I can use the Flash methods within my js file, the wmode doesn't work as planned.
After scouring the net, I have come across this post from Drupal's forums.
<object classid="clsid:d27cdb6e-ae6d-11cf-96b8-444553540000" codebase="http://fpdownload.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=8,0,0,0" id="urfront2" align="middle" height="180" width="550">
<param name="allowScriptAccess" value="sameDomain">
<param name="movie" value="urfront2.swf"><param name="menu" value="false"><param name="quality" value="high"><param name="wmode" value="transparent"><param name="bgcolor" value="#ffffff"><embed src="urfront2.swf" menu="false" quality="high" wmode="transparent" bgcolor="#ffffff" name="urfront2" allowscriptaccess="sameDomain" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" align="middle" height="180" width="550"></embed>
</object>