If you start a GTK GUI with root permissions and you notice that it uses the old GTK theme, you can make all applications started as root to use your current theme by doing this:
sudo ln -s ~/.themes /root/.themes
sudo ln -s ~/.icons /root/.icons
sudo ln -s ~/.fonts /root/.fonts
This will basically create symlinks to your icons, fonts and themes directories that draw your current GTK theme.
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Or a) use a decent version of Linux that sets things up correctly (a guy at work had old GTK windows in Ubuntu, but I don’t get it in Fedora 11 or OpenSuse 11.1) or b) if you use themes that you’ve installed yourself then move them to /usr/share/icons and /usr/share/themes instead of ~/.icons and ~/.themes (makes them available to everyone – does require sudo/super user permissions to move them)
I think I’ll try point a, thanks IBBoard for the tips.