I also had such problems with VLC on Intel HD 520, Ubuntu Gnome 16.04.1, and setting video output to GLX solved it.
** Tags added: apport-collected ubuntu xenial -- You received this bug notification because you are a member of Ubuntu-X, which is subscribed to xserver-xorg-video-intel in Ubuntu. https://bugs.launchpad.net/bugs/1537053 Title: vlc screen always on top, buggly. To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/xserver-xorg-video-intel/+bug/1537053/+subscriptions _______________________________________________ Mailing list: https://launchpad.net/~ubuntu-x-swat Post to : ubuntu-x-swat@lists.launchpad.net Unsubscribe : https://launchpad.net/~ubuntu-x-swat More help : https://help.launchpad.net/ListHelp