Thank you for reporting this issue and for providing details about your environment (Ubuntu 26.04 / BeeBEEP v5.8.2).
The "A program is still running. UNKNOWN not responding" dialog occurs because Ubuntu's GNOME Session Manager expects an immediate response to its desktop shutdown query (commitDataRequest), while BeeBEEP's system tray mode prevents it from intercepting the session manager's close event automatically.

Workaround for your system right now:
In BeeBEEP, go to Options / Preferences -> General and make sure "Prompt on quit when closing" is unchecked.
Open your terminal and check your systemd user stop timeout by editing /etc/systemd/user.conf:

DefaultTimeoutStopSec=5s

This forces Ubuntu to close lingering background apps quickly on shutdown without waiting for manual confirmation.

Fix coming in the next release:
We have identified the missing QSessionManager integration in the Qt application event loop. An update will be released shortly to handle session manager shutdown requests seamlessly on system power-off.

Tray Icon & Closing behavior:
If you want BeeBEEP to completely close whenever you click the X window button, make sure the option "Minimize to system tray when closing window" is unchecked in Options/Preferences.
If you prefer to keep BeeBEEP running in the system tray, you can leave that option checked, but ensure "Prompt on quit when closing" is unchecked so it won't block the OS shutdown sequence.