Just to note. If I run the rmiregistry from the location my .class files are generated into i.e. "F:\RMI\classes", then the Server class will run from within Eclipse.
But from what I understand, you shouldn't run the rmiregistry from the location where the class files are available, and you shouldn't have the location of the class files on the CLASSPATH environment variable that is available to the rmiregistry. The reason being that the rmiregistry will simply pick up the class files from the current directory or the location on the CLASSPATH rather than the location specified in the JVM argument -Djava.rmi.server.codebase.
I confirmed that the value of -Djava.rmi.server.codebase is being ignored when the rmiregistry is run from the directory containing the class files by setting the value of -Djava.rmi.server.codebase to an invalid value in Eclipse, the Server class still runs, which shows that the value of -Djava.rmi.server.codebase is being ignored.