Comment 22 for bug 992262

I see now what the problem is, it is the behaviour of amarok once the tray icon is disabled.
When it is disabled and removed the close button on the left will close the app. For unity music players we requested that players follow the behaviour outlined in the spec (wiki.ubuntu.com/SoundMenu).
https://wiki.ubuntu.com/SoundMenu#compliance

Amarok should just minimize on close button press and restore when activated again from the sound menu, like banshee or rhythmbox does. Banshee preserves how it operated before and handles how Ubuntu would it like it to operate by implementing a plugin for specific ubuntu UI behaviour.