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since when does qjackctl ever auto-started anyhow?

if you see all the system-tray settings grayed out that's mostly because your desktop environment doesn't support one to start with (is it on wayland for instance?) or in the other hand the Qt5 widgets framework in use are reporting that there's no support for the system-tray.

you also seem to have the JACK D-BUS interface enabled, otherwise the server prefix wouldn't appear grayed out.

please check again all your settings and options... as a last resort you can (re)move away the configuration file (~/.config/rncbc.org/QjackCtl.conf) and start from a clean slate.

hth.
cheers