I\'ve got an ASP.NET MVC application that uses jQuery. To load the js libraries, I reference them like this:
Have you tried referencing the file from the root url? I.e. instead of "../../", which has to crawl up a directoy, use "/Content/Scripts/jquery-1.3.2.min.js". This would angnostic of your directory structure.
You should also consider using google to load jquery:
http://code.google.com/apis/ajaxlibs/
You'll get much better load times.
Mike