I am not sure what is going on in your Protege 3.5 server. Some thoughts:
1. The exception is ClassNotFoundException for edu.stanford.smi.protege.server.Server_Stub. A ClassNotFoundException often suggests a classpath problem. You may want to double check the paths are right in the Java cmd.exe execution trace window.
2. Did the exception occur while the server is starting or did it occur when you tried to open an ontology in Protege client? The first line in your trace window is “Loading project plugins for project Pizza.” In my installation, when I start
the server, I get "Protege server ready to accept connections…” following that. Is it possible that you tried to open an ontology before the server is ready?
3. Did you get any error message regarding rmiregistry?