Using this in /usr/bin/compiz fixed my black window problems.
COMPIZ_OPTIONS="--indirect-rendering --strict-binding"
I also have these options in my xorg.conf in the Screen section:
Option "DamageEvents" "True"
Option "UseEvents" "True"
Option "TripleBuffer" "True"
Option "BackingStore" "True"
And at the end of my xorg.conf:
Section "Extensions"
Option "DAMAGE" "Enable"
Option "Composite" "Enable"
Option "RENDER" "Enable"
EndSection
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[nvidia-glx] Window content is black after opening 5/6 windows when using compiz
https://bugs.launchpad.net/bugs/96473
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