Where did you use the upgrade feature? I mean from where?? Did you install SMF using Fantastico? If its the case, then you must have deleted the fantastico-filelist.txt or something like that. Try manually upgrading it.
Please make a backup of the DB
SMF has an upgrade feature within the admin console.
Try uninstalling any mods you might have installed and upgrading again. Otherwise, take the steps outlines on the SMF website to perform a manual upgrade.