Using Windows Updates to install updates for your server isn't the supported way to get updates; you get presented optional updates, driver updates, etc. in addition to the high priority updates (which are all you should install).
What happened on your server to prevent the built-in functionality from working? Have you tried a server recovery? The procedure for that is in your documentation (if you have an OEM server) or you'll find a sketchy description over
here.
I'm not on the WHS team, I just post a lot. :)