I got the following error when upgrading Joomla 2.5.0 to Joomla 2.5.4.
Solution: Go to Extension Manager > Database > click the fix button / icon (on the right). This will attempt to fix any database issues.
After the fix I got the following message:
Database table structure is up to date.
Database schema version (in #__schemas): 2.5.4-2012-03-19.
Update version (in #__extensions): 2.5.4.
Database driver: mysqli.
63 database changes were checked successfully.
23 database changes did not alter table structure and were skipped.
Hope this helps!