Deleting the old server and downloading the new one, recompile, setting up (including DB) is not a good idea, I know.
The only way to fix the problem is to run the sql upgrade files.
Wait, what did you upgrade? the database or the server?
If you upgraded the database, then you need to upgrade the server (and vice versa).
Which to run? umm.. your last revision (or build date) to today (one by one)
If you just upgraded your server files, you may drop all of your database's tables and re run the sql files like you installed a new one. Be reminded that all of your data will be deleted (logins, chars, items)