Comment 14 for bug 24280

The problem is that the path that GTK searches for themes is based on the user running the program. So, if you have a theme in ~/.themes, GTK will not be able to find it when running as a different user.

As Al says, this has nothing to do with gksu, gksudo, sudo, or su, it's simply that GTK is looking for a theme that is no longer available.

Since the theme is set in gconf, maybe the theme search path could be set there too? This would solve the problem as far as I can tell.