Generally not good to include a head section in the skin file because DNN will include it's own, resulting in two head sections.
Here's some working .ascx code I have used previously, perhaps it will clear things up for you:
<script src="<%= SkinPath %>scripts/AC_RunActiveContent.js" type="text/javascript"></script>
<td valign="top" align="left" width="650">
<script type="text/javascript">
AC_FL_RunContent( 'codebase','http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=7,0,19,0','width','650','height','600','title','Cox & Schepp, Inc.','src','coxscheppnu','quality','high','wmode','transparent','pluginspage','http://www.macromedia.com/go/getflashplayer','movie','<%= SkinPath %>coxscheppnu' ); //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=7,0,19,0" width="650" height="600" title="Cox & Schepp, Inc.">
<param name="movie" value="<%= SkinPath %>coxscheppnu.swf" />
<param name="wmode" value="transparent" />
<param name="quality" value="high" />
<embed src="<%= SkinPath %>coxscheppnu.swf" quality="high" wmode="transparent" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash" width="650" height="600">
</embed></object></noscript>
</td>