I think Nautilus may have the same problem. After the upgrade, Nautilus has sprouted menus when running in the root window. The menus appear after about a short delay, just as in Gnome Terminal. Could there be a common cause?
I'm running Nautilus under fvwm (nautilus --no-default-window). I've found one other reference to this problem, but no bug report: http://askubuntu.com/questions/61105/nautilus-menu-appearing-behind-transparent-gnome-shell-menubar -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to gnome-terminal in Ubuntu. https://bugs.launchpad.net/bugs/863309 Title: Menubar always shown by default (although deactivated) (after upgrade) Status in “gnome-terminal” package in Ubuntu: Triaged Bug description: Although I have deactivated the option "Show menubar by default in new terminals" [1], it gets shown for new terminals (and has to be activated and deactivated via the "View" menu to hide it). 1: this option in located in the "Profile Preferences" (in the "Edit" menu) ProblemType: Bug DistroRelease: Ubuntu 11.10 Package: gnome-terminal 3.0.1-0ubuntu3 ProcVersionSignature: Ubuntu 3.0.0-12.19-generic-pae 3.0.4 Uname: Linux 3.0.0-12-generic-pae i686 ApportVersion: 1.23-0ubuntu2 Architecture: i386 Date: Fri Sep 30 15:36:35 2011 EcryptfsInUse: Yes ExecutablePath: /usr/bin/gnome-terminal InstallationMedia: Ubuntu 11.04 "Natty Narwhal" - Release i386 (20110427.1) ProcEnviron: LC_TIME=de_DE.UTF-8 PATH=(custom, user) LANG=en_US.UTF-8 SHELL=/usr/bin/zsh SourcePackage: gnome-terminal UpgradeStatus: Upgraded to oneiric on 2011-09-29 (0 days ago) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/gnome-terminal/+bug/863309/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : desktop-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp