Свежие новости: дело, скорее всего не в битых пакетах, а в самом flatpak. Так, при попытке создать запись в календаре, в терминале вылетают сообщения об ошибке, а само событие не запоминается:
flatpak run org.gnome.Calendar
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
[papa@comp-core-i3-3220-61992a ~]$ flatpak run org.gnome.Calendar
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed
(gnome-calendar:2): GLib-GIO-CRITICAL **: g_dbus_proxy_new: assertion 'G_IS_DBUS_CONNECTION (connection)' failed