VLC ignores some of its GUI settings. Luckily it has easy, plain text configuration.
Despite enabling the clone filter in advanced video settings, VLC doesn’t seem to want to start with the clone filter enabled. No problem, just open up
~/.config/vlc/vlcrc and look for:
# Video output filter module (string) #vout-filter=
Replace it with:
# Video output filter module (string) vout-filter=clone
That’s it. Now VLC will always start with a clone. If you want more clones than the default 2 and VLC ignores the GUI settings as well, or VLC is ignoring some other GUI configuration, now you know where to look for it.