Prototype Not Working in Window

Use the web browser to find out, for sure, what the URL is of your
popup window after it opens. View source to see what the javascript tag
looks like. Combine the two in your head to ensure that the .js file is
reachable by the combined URL.

One other suggestion - please, please do not 'bump' your post to the
top after only 50 minutes of waiting. That's just rude.