[eluser]mddd[/eluser]
You need to realize that the browser treats a CI application just like any other website. If your page is /controller/method/argument and you link to your js-files as "js/script.js" then the browser is going to look for that file in /controller/method/js/script.js. And that doesn't exist. You need to explicitly tell the browser where the file is, and not use a relative path because that will look different to the browser depending on how your url looks for each page.
One way to do this is as Clifford James points out: use the site_url of base_url functions. They will put in your site's url from config.php and make a consistent location. You could also just use absolute urls from the root of your site, like "/js/script.js". Using the functions has the advantage of easier moving around of the entire site if you want to do so in the future.
