debes de poner los dos divs dentro del mismo td, sino no saben superponerse, y el problema que estooy viendo es que tienen distintas dimensiones los td, tendras que poner estas dimensiones a los divs
supongo que mas o menos seria una cosa así
Código HTML:
<td style="width:600px;padding:5px;background-color:#FFFFFF;vertical-align:top;text-align:center">
<DIV STYLE="position:absolute; top:130px; left:100px; width:200px; height:200px; z-index:1">
<script type="text/javascript" src="menu/menu.js"></script>
</DIV>
<DIV STYLE="position:absolute; top:250px; left:150px; width:200px; height:200px; z-index:-1">
<script type="text/javascript">
AC_FL_RunContent( 'codebase','http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=9,0,28,0','width','600','height','400','src','img/pelicula','quality','high','pluginspage','http://www.adobe.com/shockwave/download/download.cgi?P1_Prod_Version=ShockwaveFlash','movie','img/pelicula' ); //end AC code
</script>
<noscript><object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=9,0,28,0" width="600" height="400">
<param name="movie" value="img/pelicula.swf">
<param name="quality" value="high">
<embed src="img/pelicula.swf" quality="high" pluginspage="http://www.adobe.com/shockwave/download/download.cgi?P1_Prod_Version=ShockwaveFlash" type="application/x-shockwave-flash" width="600" height="400"></embed>
</object>
</noscript>
</DIV>
</td>