EARs are supposed to get discovered too. I would check your agent.log file for any errors related to EAR discovery.
I'd also try deploying a very simple test EAR. If that gets discovered, then you know the issue is specific to your EAR and not all EARs.
That was it Ian. I checked the agent.log files and realized that I had it slighly mis-configured. I corrected the program and JON picked up the .ear file right away. Thanks!