This was resolved for me after shutting down and restarting. The Unity application launcher now correctly appears in front of any other window.
For me the unity&disown
solution didn't work - it actually made the entire unity UI permanently disappear until restarted, including the top part of every window with the close, minimize and maximize buttons. Even after waiting ~20 minutes the UI didn't reappear and I couldn't close any windows to see if there was possibly a dialog box waiting for my response hidden somewhere, so I had to force a shutdown by holding the power button for 4+ seconds.
The issue occurred after suspending and waking up my machine several times, although I'm not positive the two events are correlated.
Hope this helps anyone else having trouble with the unity&disown
solution.