Prova questo codice:
<DbProviderFactories>
<remove invariant="MySql.Data.MySqlClient" />
<add name="MySQL Data Provider" invariant="MySql.Data.MySqlClient" description=".Net Framework Data Provider for MySQL" type="MySql.Data.MySqlClient.MySqlClientFactory, MySql.Data, Version=6.3.6.0, Culture=neutral, PublicKeyToken=c5687fc88969c44d" />
</DbProviderFactories>