I set Elisa to remain in system tray when its window is closed. In the hamburger menu, the "Quit" entry has shortcut ctrl+q, so clicking on it completely quits the application instead of just closing the window and keep it running in tray system. But triggering ctrl+q doesn't completely quit the application and keeps it running in tray system.
I have the same bug - pressing ctrl+q only minimises the window to the system tray, but elisa closes if i press ctrl+q twice (press it, re-open elisa from the system tray, then press it again).