Just a follow up to my own problem.
I found the solution here: http://kb.adobe.com/selfservice/view...cf38&sliceId=1
My code was a bit different from the example in the link above so I thought I'd share how it worked for my specific case.
added the bold code to my existing file and now it also works in ie6:
<div>
<script type="text/javascript">
AC_FL_RunContent( 'codebase','http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=7,0,19,0'
,'width','780','height','208','src','http://website.com/swf/main','quality','high','wmode','transparent','pluginspage',
'http://www.macromedia.com/go/getflashplayer','movie','http://website.com/swf/main','allowScriptAccess','always' ); //end AC code
</script>
<noscript>
<img src="http://website.com/images/main-pic-home.jpg" />
</noscript>
</div>
They also suggest you can open your get url command into a "_blank" window to get it to work, which I tried and it does work, but that's a non-solution if you ask me. It doesn't do your visitors any good to navigate into new windows everytime they click a link. ANyway I hope this can help someone in the future.