That's by design. If you want to make changes and have them stick
install the 'simple-ccsm' package so the Custom option appears in the
Visual Effects tab. That one will not change your settings when you
switch back and forth.
** Changed in: compiz (Ubuntu)
Status: New => Invalid
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compiz settings manager lose configuration when disabling/enabling effects
https://bugs.launchpad.net/bugs/415646
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packagers, which is subscribed to compiz in ubuntu.
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