In my ASP.Net app, which is javascript and jQuery heavy, but also uses master pages and .Net Ajax pieces, I am consistently seeing on the status bar of IE 6 (and occasionally IE
I have had a similar issue before, and it was due to a long running JS piece that was in the middle of the page, the browser was waiting for it to finish executing before it would finish downloading the additional files for the site.
I'm not sure if this is an issue for you or not, but it had manifested itself in a similar manner.