I have the same issue since I recently updated both my MacBook 10.6.8 and my Mac Pro 10.7.5. In both cases CrashPlan started up and also this org.jboss.Main (which says it is version 1.0). I junked CrashPlan but org.jboss.Main still starts up everytime and shows up on the dock. I searched for "jboss" and found nothing - and have no idea idea what it is or what it does. Indeed it does, as you describe, stop me shutting down but I found that if I quit org.jboss.Main it goes away for about a second or two and then relaunches. If I quit a second time it stays away a bit longer and there is time to complete the shut down. That's my workaround.
I wish I hadn't updated - this is very annoying. Is Apple losing their grip or is it just me?!