Does this problem persist if you pass the --ignore-config option to vlc?
Also, would you mind attaching the debug output from the terminal when
you run vlc? Have you tried using --x11-display, --glx-display, or
--xvideo-display, depending on the output you are using?
** Changed in: vlc (Ubuntu)
Status: New => Incomplete
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Starts on wrong X Screen
https://bugs.launchpad.net/bugs/577246
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