when you have compiz enabled you can see some inconsistencies with the way programs minimise to the the tray. rhythmbox for example scales down and moves towards it's tray icon, just like it would if it was minimising to the window list. deluge however acts the same as if you had closed the window.
possible to sort this out? it's no biggie but consistency is a very important thing imo, especially for the novice user understanding what is going on.