Michael,
All of the ports the BIM server uses are configurable in the BIM Server Preferences. BIM Server uses one port for the Discovery feature, and 3 service ports per Module (Management, Model, Messaging). All these are configurable through the BIM Server preferences.
Port 1099 is used by default by Java RMI Registry service. ArchiCAD/ BIM Server does use Java for messaging, but you can not control Java settings through the BIM Server, and I am not sure if ArchiCAD is the only application that uses this java service.
Greg
Gergely Kmethy
VP, Customer Success, Graphisoft