I'm having similar issues, and I dunno how to fix it (the above
suggestions aren't working). I'm on Ubuntu 9.04 as well. It's nothing
to do with the desktop theme.
My problem is a bit quirkier... I had some apps open the other night
("ssh -X" windows) that overlapped the Gnome panel. I had to shut down
the computer quickly to leave (just powered down) and now the window
headers have become the new background for my Gnome panel. I dunno how
that even happened. Changing themes just keeps 'em there. It doesn't
hinder anything, but it looks atrocious and it's difficult to see many
of the icons/etc up there now. How do I get my original panel back?
** Attachment added: "Gnome Panel Screenshot"
http://launchpadlibrarian.net/36314492/Screenshot.png
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cannot change background color on parts of panel
https://bugs.launchpad.net/bugs/349774
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