No hay ningún problema, al contrario; lo que ocurre es que desde la versión 4.1, según creo, la codificación por defecto es latin1 y la collation por defecto de latin1 es latin1_swedish_ci, como puede verse en el manual.
Cita: 9.1.3.1. Server Character Set and Collation
MySQL Server has a server character set and a server collation. These can be set at server startup on the command line or in an option file and changed at runtime.
Initially, the server character set and collation depend on the options that you use when you start mysqld. You can use --character-set-server for the character set. Along with it, you can add --collation-server for the collation. If you don't specify a character set, that is the same as saying --character-set-server=latin1. If you specify only a character set (for example, latin1) but not a collation, that is the same as saying --character-set-server=latin1 --collation-server=latin1_swedish_ci because latin1_swedish_ci is the default collation for latin1.