For me, this only ever happens on the first login with a new user account. If I log into Unity first, leave it alone for a few seconds to finish initializing, and then log in to gnome-flashback, it works every time. Happened in Raring, too.
** Tags added: raring -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to gnome-panel in Ubuntu. https://bugs.launchpad.net/bugs/1232299 Title: gnome-session-flashback with Compiz launches Unity Status in “compiz” package in Ubuntu: Confirmed Status in “gnome-panel” package in Ubuntu: Confirmed Bug description: gnome-session-flashback (Flashback (No Effects)) which runs with Metacity works fine. gnome-session-flashback (Flashback) which runs with Compiz starts Unity instead. It works very well with Metacity, but if you use Compiz, then you get a conflict with Unity. That is; you get both Unity and Gnome Panel running at the same time. ProblemType: Bug DistroRelease: Ubuntu 13.10 Package: gnome-session-flashback 1:3.6.2-0ubuntu15 ProcVersionSignature: Ubuntu 3.11.0-8.15-generic 3.11.1 Uname: Linux 3.11.0-8-generic x86_64 ApportVersion: 2.12.5-0ubuntu1 Architecture: amd64 Date: Sat Sep 28 01:18:08 2013 GsettingsChanges: b'org.gnome.gnome-panel.run-dialog' b'history' b"['compiz', 'ubuntu-bug fontconfig', 'update-manager -c -d']" InstallationDate: Installed on 2011-10-21 (707 days ago) InstallationMedia: Ubuntu 11.10 "Oneiric Ocelot" - Release amd64 (20111012) MarkForUpload: True PackageArchitecture: all SourcePackage: gnome-panel UpgradeStatus: Upgraded to saucy on 2013-09-16 (11 days ago) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/compiz/+bug/1232299/+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