I've recently changed my MU root domain. I've just noticed that I can't install any plugins any more (dashboard included) using the 'install' feature. Whenever I try, I get to choose from 2 domains (as if they were two separate sites) - the old one, that redirects to the new one, so nothing's accomplished, and the new one, which - upon choosing - returns an error: plugin package not available.
As for now, only one domain is "pinned" to WPMU - the old one. That's because I've uninstalled the dashboard (so the new domain isn't listed), but WPMU still thinks the old domain is a separate site where everything's like before I changed the root domain, which of course is false. We've got some internal conflict going on here, but there are no references to the old domain in the database, so I'm guessing maybe it's on your side.