I've been trying to get my intranet password working again since I changed it a week or so ago. It worked in Safari 2, and after upgrading my G4 laptop to Leopard it still worked fine. It was only when I needed to change it that I found I couldn't change it and save it.
Long story short, it's broken in Safari to at least 3.0.4. See: http://discussions.apple.com/thread.jspa?messageID=6283882
Even if you open Keychain Access and set it manually, it won't work. A big shame. It's odd how it only stopped working when I had to change the password.