Tray icons are enabled but, there are some apps (i.e. amarok) that allow you to close them and stay only as a tray icon, and after show them up (before really closing this app). Ksmoothdock has a little problem with this: tray icons are shown, but if you close the app (i.e. amarok), this icon dissappears (even though app is still running).
Another important thing with tray icons with ksmoothdock is: Some apps (like kopete, amarok, etc..) wich has their own tray icon, has a context menu if you right click on it (in kicker's tray icon) but in ksmoothdock tray icon, it is only shown for all: minimize, maximize, restore and close options for all and the context menu isn't there.
Please tell the developer of the application about this problem. Nothing we can do here.