I found what the issue was, it is something related to qt-config. The issue is
something to do with qt4-qtconfig package. Please check it out and fix it.
Here is a discussion on the topic in VLC forum
http://forum.videolan.org/viewtopic.php?f=13&t=67709
** Changed in: vlc (Ubuntu)
Status: Incomplete => New
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VLC 0.8.6c does not save playlist on Gutsy
https://bugs.launchpad.net/bugs/136358
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