If you are not using the plugin, it looks like you're using it's swfobject.js file.
It may be that the plugin's version of the file is customized to work as a plugin (uses hooks that correct for permalink differences).
Maybe if you tried a more generic version of the swfobject.js file?
http://wordpress.org/extend/plugins/flash-video-player/ As the plugin uses
if you aren't using the plugin file as a plugin, why not try the original files it uses? Or maybe there's another plugin that can be used in the template that you could use as a plugin without needing to hack the header.php file or mess with the permalinks?
Maybe the "Kimili Flash Embed" plugin. http://kimili.com/plugins/kml_flashembed
I’d like to use KFE to put a Flash header in my Wordpress site. How do I do it?
Unfortunately, the way Wordpress processes the plugin doesn’t allow you to use a kml_flashembed tag in your page templates. It only works in article posts.
Not any more. Starting with KFE version 1.1, you can put a kml_flashembed tag anywhere on your site. Posts, page templates, in headers, on sidebars—anywhere.