I have tried to repair tables without errors and run the mysqldump but the result is the same.
The database is with greek characters. However I have moved other databases with greek characters to the same server without running into this problem.

Have you checked this mysql bug reported: http://bugs.mysql.com/bug.php?id=20710 ?

It happens I have version 4.1.20. How can I walkover this without upgrading mysql?