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 Bugs, which is subscribed to 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 -- ubuntu-bugs mailing list [email protected] https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
