Logging in from multiple places has always been terrible. I'll be logged in on Mac and available but randomly get emails as if I'm offline. I'll be online on my phone and get e-mails. I wan't emails of messages when I'm actually offline and not logged in but HipChat doesn't seem to care and emails me anyways sometimes. The option to turn off email notifications isn't very configurable either. Its off or on.
Look at the release notes for windows and mac and search for reconnection. Just about every release has a fix for reconnecting going back to 2014.
https://www.hipchat.com/release_notes/mac https://www.hipchat.com/release_notes/windows