I have not seen this before, where it looses the ability to invoke EJBs.
You are saying the jboss instance cannot invoke other EJB's from a different machine (likely running jboss also?) and clients are unable to remotely invoke EJBs on that jboss server that is having the problem after the Nessus scan?
What are the errors you're seeing when the jboss server is unable to invoke a remote EJB running on another (jboss?) machine?
What error do you see on the client side when it is unable to invoke EJBs running on the jboss instance that is having problems?