I have a dual head setup with two monitors connected to my graphics card, with two completely independent X screens.

after starting the settings mangager on the second screen, it starts up nicely, but many configuration items appear on the first screen.

display: is completely displayed on the first screen
desktop->behaviour: the menu editor is displayed on the first screen
user interface->font: the font selector is displayed on the first screen
preferred applications: is completely displayed on the first screen
file manager: is completely displayed on the first screen
window manager->font: the font selector is displayed on the first screen
panel: creating new panels moves the window to the first screen
notification settings: is completely displayed on the first screen
sound: is completely displayed on the first screen