You could always try Opera for a third opinion. Seeing as it's not a browser problem, or a network problem, the only thing that I can imagine causing it is some sort of proxy inbetween your browser and the web.

Hmmm... Do you have problems with links that aren't javascript? Also, make sure you realize that javascript has nothing to do with Java. Javascript is the thing that's most likely to get mangled by a popup blocker, as it'll thin the javascript is a popup. Perhaps go through the task manager and try killing tasks until you can't kill any more. (this requires some finesse, as you've got to avoid the essential ones) and then see if the problem is the same/better/worse.

Someone at my office just dug up a how-to-reinstall-windows-xp-networking MS article, which I can try and find for you if you think it would help. We've been growing increasingly annoyed at XP's inability to reinstall all it's networking components, so it was a welcome find. I havn't actually tried it out yet though. It couldn't really make things much worse, however.

Matthew