I’m glad I’m not the only one with the problem of duplicate instances of Atom (the text editor) opening on me. For me, it seems to happen when an update is imminent and I’m opening a file from an FTP client. The second instance almost always crashes and then I have to do a dance of reopening Atom and my FTP client several times until things begin working properly again. Or I just force the FTP client to use another editor until I have time to deal with it.
Hopefully, they resolve it. Perhaps the reach of the tweet of an Eric Meyer will help the cause.