I think these are one in the same. the startup processes are called when user logs on. these are usually run and runonce. if its not in those, it wont start on startup.
I dont think anything else can be set in the registry to load up automatically. That would probably be a security issue if it could.
Are you having an issue with security? a program loading that you cant stop? or trying to develop a program or set one up to load on startup without using run location?