Comment 17 for bug 45544

I've been looking into this and figured it out that the problem is somewhere in the 03_fix_xinerama_stack_c.patch patch for the notification-daemon. I built packages of the new release of libnotify 0.4.5 and notification-daemon 0.4.0 in my PPA hoping the fix would be in the new release, but after installing them I saw the same problem. I rebuilt notification-daemon without the 03_fix_xinerama_stack_c.patch patch and the notifications don't overlap the panels anymore. It might be better though to figure out where the problem is exactly in the patch instead of removing the entire patch.