I understand what is happening now (thanks to Trent W Buck). On the current default desktop configurations, applications such as Evolution and gnome-screensaver bring in a cursor theme by default (such as dmz-cursor-theme in Squeeze). On the cursor theme, the mouse pointer colors can no longer be changed. To restore the classic behaviour, it is just a matter of turning off the icon theme (set in /usr/share/icons/default/index.theme), but of course this means going back to the original cursor graphics.


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