Description of problem:
The agent binaries can be manually edited to supply default configuration values. This allows agents to start up and skip the initial config and registration steps.

Link:
http://docs.redhat.com/docs/en-US/JBoss_Operations_Network/3.0/html/Installation_Guide/preparing-a-preconfigured-bundle.html

However, when the server is upgraded, those edited binaries are lost, so subsequent agent installs don't have the custom config.

This should be noted in the server and/or agent upgrade sections, that if you had an edited agent binary, you need to edit it again.

Additional info:
Bug 781586