Hi umeshvn,
It's because of the way IIS handles the request to jquery.js. IIS assumes that resources such as .js, .jpg, etc, are all static resources, and thus doesn't need to pass them through the ASP.NET engine. In order to to prevent this from occurring you can add a line to the web.config for a path that you want IIS to leave alone.
<system.webserver>
<handlers>
<add name="scripts" path="/Scripts/*" verb="GET" type="System.Web.Handlers.TransferRequestHandler" preCondition="integratedMode,runtimeVersionv4.0"/>
</handlers>
</system.webserver>
Or
Use the following sytax to link you CSS/js files.
<link rel="Stylesheet" href="<%=ResolveUrl("~/Styles/site.css")%>" />