Gemini JPA currently always refreshes a bundle when using the configuration admin service to configure it without regard to the REFRESH_BUNDLES system property. Is there a reason to do so? This raises some race conditions that can lead to deadlocks with iPOJO and Felix.
The REFRESH_BUNDLES property was created for the listener to not refresh bundles when it detected them. It was not designed to stop refreshing for the config admin service, which is a different case for refreshing. There are probably cases when users can create conditions to not require a refresh for a standalone config, though, so either we could extend the global refreshing property to apply to this or use the gemini.jpa.punit.refresh property to disable it for standalone configs. Feel free to enter a bug on this: https://bugs.eclipse.org/bugs/enter_bug.cgi?product=Gemini.JPA