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So the controls of VLC are gone and so is the menu in the upper corner of the screen. I already reinstalled it two times: once with the Ubuntu Software Center and it didn't work, so I tried with terminal with these commands:
sudo apt-get purge vlc vlc-nox sudo apt-get install vlc
This way didn't work too. I am currently on Ubuntu 13.04 (64 bit version) with the proprietary Nvidia driver 313, the system is also dual-boot with Windows. This whole thing happened today after update of the OS, as far as I know there was no problem yesterday, it must have been from the update I think. The player itself is working (playing movies, rewind, pause), but as mentioned the menus and controls aren't displaying, as well as the context menu when right clicking.