For what it's worth, this isn't limited to Ubuntu. I'm running Gentoo 2006.1 with Gnome, and have been having this exact problem with Amarok ever since I installed it. Perhaps this should be filed as a Gnome or KDE bug?
-- Gnome-panel flashing for kde apps on workspace change https://launchpad.net/bugs/78511 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs