I ran into the same problem, fortunately in a test environment. In my case I was able to determine that the problem was caused by the security configuration I use.
Normally, my wp-config.php database user is a limited user that doesn’t have rights to create tables. I mistakenly ran the update.php script with that user still enabled, and apparently, while part of the script failed, part of the script succeeded. Thus, when I re-ran it with the “dba” user enabled, it didn’t do everything it needed to do.
I found a fix that worked, at least on my system, which was to drop the database, reload it from the just-before-upgrade backup and re-run the update.php script using the “dba” user.
Hopefully: (1) I won’t have the same problem on my live site, and (2) this information is useful, either to users with the same problem, or to someone trying to produce a general fix.
