not sure if the box I was having problems with was 0wned or not, but I've seen something like that happen when you use a not so intelligent software firewall and unusual network configuration. for example, having two routers hooked up together (one being set in switch mode) can cause firewalls to silently block all or more mind-bogglingly just some web requests. in my case when I dug deeper I found the firewall was logging some sort of ICMP based attack. i didn't have much luck with tweaking either of the two firewalls I tried and ended up having to uninstall them.
i had tried using Sygate Personal Firewall which while old and probably no longer very secure, it was pretty nice. i had also tried Sunbelt which was thoroughly overcomplicated and not fine grain enough for ignoring specific false positives. the symptoms I saw were the "internet" was not working (YahooMail not authenticating OR the actual emails not opening) while most of everything else worked, except when it was everything that actually would not work.