i have my 27" iMac set up to use 4 desktops which i three finger swipe between. I do different things in each desktop (JRiver in one, Mail and iMessages in another, Productivity apps in a third, etc).
The pop up displays only on the desktop where JRiver is running. It might be nice to have a setting to allow it show up in every desktop.
To be clear, i'm not talking about multiple monitors, just desktops which all display on my iMac.