I have just experienced the same problem upgrading an 1.2 wordpress installation to 2.0.1.
I noticed that the upgrade script failed to upgrade the scheme for the wp_users table.
I didn’t have much time to fully backtrace the problem (I guess it had something to do with database user UPDATE permissions).
I made up the following quick solution:
temporarily set a user with full permission for use in wp-confing.php
changed the value to db_version record to something less than 3308 an greater than 2541. I randomly selected 3300.
rerun tha upgrade script.
Database schemas got updated and now everything works as expected.
hope this helps somebody
