Thanks for your response, Ryan. Just to be clear, I'm using the QB desktop app, and not QBO, in case that makes a difference. 

There isn't anything on my system that is automating the QB app and I don't have any shortcuts set to QB. 

It seems like a bug in the system.

It goes like this:

QB is shut down completely and I'm working in another program (ex. Final Cut Pro.) Shift-Command-B is a shortcut in FCPX that I use all the time. When I use that shortcut in FCPX, it will sometimes randomly open the QB app.

And sometimes, if QB is already open, Shift-Command-B will open another instance of QB so there are 2 QB windows open. 

Have you heard of this?