I'll pass that on to the engineers.
If you go to your one-click install page - https://panel.dreamhost.com/index.cgi?tree=goodies.installer& - and click on 'Manage installed Applications', you can expand the items and see if auto-upgrade is turned on. It's a little obscure, indeed, and we've been working on ways to make that both more obvious and intuitive.
Keep in mind, with Joomla (and a lot of similar products), not upgrading promptly can leave you vulnerable to security breaches. It's encouraged in the Open Source community that hosts upgrade people to protect not only themselves, but everyone else on their servers. This, of course, makes it way too easy to argue both sides of the issue Do we make the 'This will auto-upgrade!' alert big so people see it, or do we not because they may turn it off without understanding the ramifications. There's no one perfect answer, alas!
The fix was still running yesterday when I logged off, but it should be done today. If you're still having the problem, update your ticket with us and ask if they can have it run manually for your site.