you need to look at the agent logs and find out if there is anything odd with discovery. RHQ_AGENT_DEBUG=true might help
I suspect what is happening is your running JBossAS instances cannot be discovered because they have been started in some uncommon way (i.e. are you starting them with a native Java Service Wrapper? your own start script?).
Use the agent's "discovery" prompt command to help you figure out if the plugin can discover them ("help discovery" for more)
Yes they all are configured as a windows service with jboss-native.
Then the auto-discovery mechanism can't find it. The Jopr agent's jboss plugin makes an attempt to find running JBossAS instances but it can't find all of them running because they may be running differently (like in your case).
You can "manually discover" them in this case. Go to the inventory tab for your platform and go through the manual discovery process to add the JBoss instances into inventory.
There is documentation available on how to do this. Somewhere here: http://www.redhat.com/docs/en-US/JBoss_ON/
If you want, describe your exact startup setup and we'll see if it makes sense to add more code to the jboss discovery component to help auto-discover these.