Y por eso te digo, en la documentación dice:
Cita: How table and database names are stored on disk and used in MySQL is affected by the lower_case_table_names system variable, which you can set when starting mysqld. lower_case_table_names can take the values shown in the following table. On Unix, the default value of lower_case_table_names is 0. On Windows the default value is 1. On Mac OS X, the default value is 2.
lower_case_table_names system variable, which you can set when starting mysqld.
La variable del sistema lower_case_table_names,puede ser cargada cuando se inicia mysqld.
Esa es la forma de cargarla y configurarla.