Originally Posted by venom1st
If this doesn't help, you probably still have ISAM tables in some of your databases, have a look at the output of mysql_upgrade and/or search for ISM and ISD files within your database dir (usually /var/lib/mysql).
mysql_upgrade -u root -pPASSWORD
If there are some of these, bad news, ISAM is no longer supported by MySQL (>=5.x). You need a 4.X MySQL server to convert ISAM tables into the MYISAM format (ALTER TABLE isamtablename ENGINE=MYISAM). Or, probably easier, drop the databases which still have ISAM tables and load your last, flat sql dump of these databases.
find /var/lib/mysql -name *.ISM