This also breaks my workflow. I use keystrokes to toggle my Mac apps in and out of view using the Alfred app's quick launcher ability. With Evernote, everytime I toggle it back on it brings the minimized or closed main window back on top of the note I was working on. If it wasn't for a useable solution I discovered, this issue would have caused me to abandoned Evernote.
The solution for me was to NOT minimize or close of the main window. Instead I cover the main window with the note I'm working on. Since I'm toggling the app, it hides both windows when I toggle it off, and shows both wind