No probs here with the Duality pref pane, aside from it not handling some themes (the 10.2 vs. 10.2.3 in the script issue). I've switched themes with it dozens of times, and never had any system mess-ups.
I've also used ThemeChanger for those "stubborn" themes, and no probs with TC either.
I've also used ThemeChanger for those "stubborn" themes, and no probs with TC either.