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I haven't tried this in a while but looking at what you wrote and looking back at http://jayshaughnessy.blogspot.com/2013/03/store-your-rhq-agent-preferences-in-file.html, it seems you've done what you need to do. Looking at the code it would seem that for some reason the -Drhq.preferences.file is not getting picked up, because the code is pretty straightforward.
If I get the chance today I'll give it a try. You may want to try from scratch by removing the service (rhqctl remove --agent) and then re-installing the service (rhqctl install --agent). Maybe save the current prefs file in a safe place so you can reference values you may need.
Actually, this setup is for a standalone agent (no the one that gets installed on the same machine with the RHQ server). Let me know if you can replicate this issue.
I used a workaround by relocating the Java Preferences store location by using the java.util.prefs.userRoot property. This way, even if the user home directory is shared on NAS, each agent has its own private preferences store.
did you happen to read the docs and FAQ on this stuff? Just for the record:
The FAQ (there are several sections that refer to the preferences):
Here's an agent page on it:
Yes, I did but these were not helpful in resolving my issue.