Let me rephrase it more specifically to work with the various customizations you've made on your site.
replace the contents of your /incluedes/templates/template_default/jscript/flashheader.js file with this:
HTML Code:
document.write('<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" ');
document.write(' codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=7,0,19,0" width="950" height="200">');
document.write('<param name="movie" value="flashheader.swf" /><param name="quality" value="high" /><param name="wmode" value="transparent" />');
document.write('<embed src="flashheader.swf" width="950" height="200" quality="high" pluginspage="http://www.macromedia.com/go/getflashplayer" type="application/x-shockwave-flash" wmode="transparent"></embed>');
document.write('</object>');
The additional <script> etc tags in my prior post were referring to the ideal "end result" ... rather than the exact line-by-line changes to make.
The above should accomplish what you're after with minimal changes to the rest of what you've done.
The javascript method you've employed is one of a few different ways to auto-activate flash objects on a website. I'm not certain this is the best way, but it works.