I want to thank you for your incredible feedback. With your help we were able to reproduce the two issues you saw, namely the random disconnect and relaunch of the 'new remote wizard'. This one has been driving me insane but I could never find a way to reproduce it reliably.
App updates are automatically done within the app, if you launch it, the app will check. If you are subscribed to the beta forums, you should get notifications when I create a thread. We've released a new version, hopefully this is going to be a lot better: https://forum.flirc.tv/index.php?/topic/10385-skip-app-v0966-beta/
Please post version specific feedback there. Will lock this thread in deprecation.