I can reproduce that with a fresh install of Arch in a virtual machine. Gnome desktop and conky, with conky being put into autostart using the tweaks tool of the Gnome desktop. Have a look:
As the output of ‘ps’ shows, conky is definitely running, but it is not being displayed. Changing anything in its config, and then changing it back and saving that config makes it reload, and being displayed – same as if you ‘killall conky’ and reload it using the meta key and its icon.
Does not happen in Debian Trixie, but even with ps and pstree as well as Gnome Mutter’s ‘Looking Glass’ debugger I can’t figure out where the differences are. Happens only in Wayland, not when logging in using X.
Hints, anyone? Thanks 🙂
Update, from Wed 6 Aug, 2025: filed a bug in Arch concerning this…