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when I configure unity via CompizConfig Settings Manager or dconf, the settings can be seen like they applied but unity doesn't care

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I just ran into this problem, try logging out and back in and see if the settings take.

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If a log out/in still doesn't show changes then maybe you are using unity-2d instead of unity(3d) There are many ways to tell, to save time & typing just run this in a terminal, will be obvious

ps aux |grep unity

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