After installing Messaging Server 6.3 64–bit Edition and running the comm-dssetup.pl script, run the configure program to create an initial runtime configuration to complete your installation and initial configuration of Messaging Server. For example, if you installed 64–bit Messaging Server, run /opt/sun/comms/messaging64/sbin/configure. For detailed instructions, see: Creating the Initial Messaging Server Runtime Configuration in Sun Java System Messaging Server 6.3 Administration Guide.
Creating an Initial Running Configuration is only for new configurations, not for configurations created with the migrate-config tool which is described in Upgrading Messaging Server.