It'll be a browser issue then. Server responces are very generic responces. If IE's timing out, than IE isn't liking something being returned and having a cow.
Sometimes it can be fixed server side, but you need to figure out exactly what's causing the problem (local proxy with logs turned on). Or you can fondle with things on your site to see if you can "fix" IE.
Using any form of SSL stuff? I know IE has a cow on our intranet and it's more SSL / IP resolution/routing crap IE does.