I believe I have a similar issue with MySQL. We have the following class

public class User {
  ...
  @Id
  @SequenceGenerator(name="seq_user", sequenceName="seq_user")
  @GeneratedValue(strategy= GenerationType.IDENTITY, generator="seq_user")
  protected Long id = null;
  ...
}

Starting with an empty schema, the user table and the seq_user tables are created, but no initial value is inserted. This is not the case with v4.3.10.

I have enabled logging on the MySQL server and with version 4.3.10 I see the following line:

insert into seq_user values ( 1 )

There is no such entry when using version 5.0.1.

The MySQL server logs are attached.