I had this issue on 12.04, and I believe on 11.10 before that...but have made it go away by switching between Desktop Cube to Desktop Wall and back to Cube in ccsm (which requires disabling and re-enabling unity, so not entirely recommended I guess!)
In the process I noted that I had Gnome Compatibility enabled, and there was a conflict with Unity...somewhere along the line whatever was leading to this unity-always-on-top behaviour got cleared out, but I'm afraid I don't know exactly what it was. -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/931460 Title: Unity panel displayed on top of full-screen windows To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/unity/+bug/931460/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs