In 1.2.11 on Linux, there's no way to quit upplay, except for killing it through system tools.
Pressing CTRL+Q or clicking on File -> Quit only closes the window, but a tray icon persists. Right clicking on the tray icon and then selecting Close doesn't close upplay.
This behavior is independent from the preference "Close to Tray", i.e. that preference has no effect.
This seems to be a regression, as the problem was not present in upplay 1.2.9
