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 working differently. My desire would be to bring back the window I was working on. Other details: this is Evernote 5.6.0 (and also whatever I was running before I updated) on OSX 10.9.5.