Experimente estes http://dev .mysql.com/doc/refman/5.5/en/optimizing-innodb-bulk-data-loading.html
Talvez seja um problema de autocommit, desligue isso e veja o que acontece.
SET autocommit=0 ; source <your dump file> ; COMMIT ;
SET autocommit=0 ; source <your dump file> ; COMMIT ;