Re: Can someone write me a script
This is a bit of a problem with Compiz-Fusion's configuration as of 8.04.
I can't say this definitively, because I'm not on Ubuntu at the moment, but I fixed this by setting the window decorator (System>Prefs>Advanced Desktop Effects Settings (ccsm-advanced or advanced-ccsm, one of the two, apt-cache search ccsm will bring it up)>General (or something to that effect)) to emerald --replace.
I guess the GTK window decorator loads before Compiz Fusion kicks in, so emerald alone won't replace it. If you want emerald --replace to run every time you change a theme, well, I don't think you can do that, and its not needed either, because emerald auto-loads the themes you select in the theme manager.
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