I have tried to put a Flash-file in a page, but EpS won´t show it. I copied the OBJECT/EMBED code snippet into the page. I tried with a http-URL and a relative one. I have also tired to put he swf directely in the templates folder.
Have you tried to view the source from the browser when the page is in "view" mode?
Sometimes the XHTML-editor format/change the text/code in the editor when saving the page. Simular effects appear when trying to add JavaScript in a XHTML-editor.