Looks like the tray problem is still evident in Beta release v4.9.16. I still see both the taskbar button and the tray icon on minimize. However if I choose the "Exit After Transfers" option then Limewire successfully minimizes to the tray only.

An option within Limewire to disable the tray icon completely would be great. Since I use the kdocker utility on KDE I would rather let this control my system tray icon because it also lets me choose a custom tray icon.