How to force quit an app that doesn't show in the Force Quit Applications menu?
The Force Quit menu will only show foreground windowed applications, not all processes.  Launch Activity Monitor, and search for the name of the app, or look for processes marked in Red with "Not Responding". There is a Quit button in the toolbar, where you can choose to Force Quit a process. 

Items in the menubar are sometimes controlled by the SystemUIServer process, which may also need to be restarted.