Sorry to rain on people parade but I believe I have found a much more simple solution.
Go to the tinymce.js file and replace line 68 window.tinyMCE.execInstanceCommand('content', 'mceInsertContent', false, tagtext);
with
tinyMCEPopup.editor.execCommand('mceInsertContent', false, tagtext);
I got it working, our company uses 3 different servers and so line 69 of the flowplayer.class.php files was set to $plugin_url = str_replace($_SERVER['DOCUMENT_ROOT'],'',$cwd);
This was generating an icorrect link to flowplayer-3.1.4.min.js.
I have since changed line 69 to $plugin_url = get_bloginfo('wpurl')."/wp-content/plugins/word-press-flow-player"; and now have no issues.
