Would you mind creating a separate thread on AnswerHub for this to make it easier for user support folks? Thanks.
We’ve seen this issue in the past and it looked like a bug in OS X that seems to be fixed in 10.12 , but we never had a solid repro, so we could never properly investigate this. We think that Cocoa’s NSApp object was not releasing something on exit in some circumstances and the process hangs in this weird state where it’s still shown in the Dock, but not in Activity Monitor, etc. Without a good repro it’s very hard to figure out what we’re doing in the engine to put NSApp in this state.