I had this problem today. I opened an .flv and the colours were similar
to the bug report. I managed to fix it by switching the video output to
X11 in VLC preferences: Video > Output Modules > "X11 video output"
(need to have advanced options checked). It was set to Autodetect but
presumably this decided to choose something other than X11 for a change.
Putting the setting at "XVideo extension video output" makes the colours
go awry again.

Interestingly, I had the problem affected Totem movie player at the same
time. I fixed this by running "gstreamer-properties" and in the video
tab switching the default output plugin from Autodetect to "X Window
System (No Xv)". A pattern emerges...

Note: I'm using proprietary nvidia.

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vlc video colour change
https://bugs.launchpad.net/bugs/199975
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