How can I get the mediaelement.js to work in a popup window?

Question

I got the Media Element JS player to work, but when I tried to get it to play in a pop-up, I noticed that it breaks the popup. It looks like I can't call JavaScript inside a JavaScript. My popup is pretty simple, it just does window.open and uses document.write with code to build a new page with its own style sheet. However, I can't load the mediaelement.js stuff inside that. Maybe I should just load the Flash that comes with it? There's also a silverlight file.

Can someone please help? I need a player that doesn't require an XML file for the playlist, works in all browsers, plays MP3s and has a timer on it. I've been working on it all day to no avail!