When I change settings (Settings > Notifications > Clear the Show a popup checkbox), they are remembered for the current session only. When I quit Hipchat and restart, it returns to default settings.
Interesting, by default HipChat should keep your settings modified, that's definitely not the expected behavior. It seems like you're running into some kind of issue or bug. Can you please file a request with HipChat support at support.atlassian.com? An issue like this would require some testing and further investigation by the support team. Hope that helps.
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