Are those instances pointing to the same jboss-as directory structure?
Jopr is looking for a java process in the process table that has org.jboss.Main as argument and goes from there, so it does
not depend on the run-script itself.
You'd need to have a look at logs/agent.log on the agent and see if it creates messages around that jboss instance.
If you've found them, you can post them here (if they don't immediately give you a clue).
To trigger the log messages you can kick off a discovery scan by running the following command from the Agent prompt: