I don’t think that this was caused by the kernel update (I even booted up the old kernel to make sure), but some other update that came along recently is probably to blame, and the problem didn’t show itself until I had to log out and log back in.

I don’t use a fancy theme, just the regular default Ubuntu theme.  In this situation, the window borders were still themed properly (although now an ugly blue color, which you can’t see in this screen shot), but the icon set was the default GNOME set no matter which set I chose in the appearence preferences, and most of the controls weren’t themed either (see the bottom-left and top-right of the screen shot).

I thought that maybe something had gone bad in my profile, but I created a new account and it also had the problem, so something had apparently broken system-wide.  This is what makes me suspect that a recent software update is to blame, because I haven’t been poking around in any system-wide stuff on this machine in a while.

I didn’t realize that using the FreeNX server was part of the problem at first, but I finally found some other people who have the same issue this evening, and one of them mentioned this bug report, which mentions another bug report, which has the solution to the problem.  (It doesn’t just affect FreeNX either, some people have the same problem with VNC.)  It turns out that gnome-settings-daemon is crashing, and without it running, the theme is messed up (among other things).  To get it running again, you have to disable its keyboard plug-in.  (I’m not yet sure what you lose by disabling this plug-in, but the keyboard still works even without gnome-settings-daemon running, so what’s there to lose…).

Here’s the solution.

• Run gconf-editor
• Navigate to /apps/gnome_settings_daemon/plugins/keyboard
• Uncheck the “active” box on the right
• Log out and log back in (or manually start gnome-settings-daemon)

There you have it.  This will tie us over until the issue is actually fixed in gnome-settings-daemon.  Maybe, if you are experiencing this issue, you didn’t have to search around for as long as I did to find the solution.

Update: August 5, 2009

There is a new bug report on this issue.

Also, a user reported that the fix above did not work.  I suggest also disabling the mouse plug-in for gnome-settings-daemon (by following the steps above, but going to /apps/gnome_settings_daemon/plugins/mouse instead), since some of the comments in the first gnome-settings-daemon bug report indicated that this was necessary for them to fix the problem.  If that doesn’t help, then something else is causing gnome-settings-daemon to crash… or if it is not crashing, you must have a completely different issue.

Update: September 23, 2009

Reportedly, you can fix this problem by reverting libxklavier to version 3.9-0ubuntu1.