No user groups when luching from krunner (systemd --user)

Groups are inherited. If you changed your groups, the existing session processes will continue to fork new processes with the old groups. If you changed your groups and logged out, it might still be that some KDE components (e.g. possibly kded or dbus-daemon) did not immediately shut down and were actually re-used for the subsequent login, so if apps are being started indirectly, through those components, they'll continue inheriting the old groups.

In particular, KDE and GNOME might launch applications through the per-user systemd --user service manager – which runs in background (unassociated with any specific session) for as long as you have any sessions, and exits ~10 seconds after all your sessions have been closed. The same applies to dbus-daemon as long as it is managed by systemd.

Log out, then wait ~30 seconds before logging in again. Alternatively, log in to console (tty) and run ps axf to check what leftover processes you might have running. (If the systemd manager has too many leftover KDE processes running, systemctl --user exit should clean it up.)