It kind of sounds like a bug in the upgrade code, but I haven't seen any other reports of this problem.
The fact that they are not there makes me wonder what else you might be missing.
Check to see if you have the file:
setup/includes/upgrades/mysql/2.1.0-rc-1.php
If not, see if you can find a copy of it (it should be in the 2.1.0 package) and put it there. Then run setup again and see if that fixes things. My guess is that it didn't execute during the install. If you look in the file, you'll see that it does a bunch of other necessary stuff including changes to the user table.
If that doesn't work, as a last resort you might try putting the file in place and creating a snippet with this code:
<?php
return require 'full/path/to/2.1.0-rc-1.php';
Then put a tag for that snippet on a page and preview it. I'm not guaranteeing the results though.