IMO, could be a couple of this and it may have nothing to do with IE. I would try a trace route the site you're having trouble with to see if there is a time out on any of the 'hops' the request takes on the different servers between your PC and the site itself. If it makes it all the way there, I'd suspect a browser issue. If not, you may want to contact your ISP with the information to see if the is a routing issue and see if they can contact the hosting company where the request times out. They can also help determine if it's a reverse DNS issue. You can try looking into this as well by typing in the actual IP address( if you know it) of the site you're trying to reach in your address bar..if it displays the page, something in the browser or the site itself is unable to resolve the "names" of the page with the IP ( what the "real" name of the page on the internet is) or you could have multiple winsock files on your PC that are cuasing a conflict.
Just my $.02