Thanks for looking at this and asking for clarification! I can confirm that this happens on my system with minimize/yellow/cmd-m. The note-specific window appears instantly and a moment later (maybe 1/4 of a second) the main window is also restored, on top. I also tried closing/red/cmd-w and it also brings back the main window (as you also noted.) I can get the desired behavior (restore the note that I was working on, leaving the main window minimized) by right-clicking the Evernote dock icon and choosing the note specifically. But this is extra clicks. Good point about different apps